Epigenetic transgenerational inheritance of altered ... - Semantic Scholar

Epigenetic transgenerational inheritance of altered stress responses David Crewsa,1,2, Ross Gillettea, Samuel V. Scarpinoa, Mohan Manikkamb, Marina I. Savenkovab, and Michael K. Skinnerb,1,2 a Section of Integrative Biology, University of Texas at Austin, Austin, TX 78712; and bCenter for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164

Ancestral environmental exposures have previously been shown to promote epigenetic transgenerational inheritance and influence all aspects of an individual’s life history. In addition, proximate life events such as chronic stress have documented effects on the development of physiological, neural, and behavioral phenotypes in adulthood. We used a systems biology approach to investigate in male rats the interaction of the ancestral modifications carried transgenerationally in the germ line and the proximate modifications involving chronic restraint stress during adolescence. We find that a single exposure to a common-use fungicide (vinclozolin) three generations removed alters the physiology, behavior, metabolic activity, and transcriptome in discrete brain nuclei in descendant males, causing them to respond differently to chronic restraint stress. This alteration of baseline brain development promotes a change in neural genomic activity that correlates with changes in physiology and behavior, revealing the interaction of genetics, environment, and epigenetic transgenerational inheritance in the shaping of the adult phenotype. This is an important demonstration in an animal that ancestral exposure to an environmental compound modifies how descendants of these progenitor individuals perceive and respond to a stress challenge experienced during their own life history.

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henotype is determined by both inherited and experienced factors. Traditionally, the former are regarded as a result of genetic inheritance, and the latter encompass events in the individual’s personal life history. Study of how the environment shapes the phenotype was initially referred to as “epigenesis” (1) and later termed “epigenetics” by Waddington (2). The current definition for epigenetics used in this study is “molecular factors or processes that regulate genome activity independent of DNA sequence and are mitotically stable” (3). The model used in the current study involves an epigenetic transgenerational inheritance of a behavioral phenotype (4) induced by an environmental toxicant (5) and transmitted through the germ line, involving a permanent alteration in the sperm epigenome (i.e., DNA methylation) (6). The epigenetic transgenerational inheritance of this altered sperm epigenome modifies the subsequent development and epigenomes of all cells and tissues, including the brain, to promote phenotypic variation (7). Although no direct epigenetic measurements were made in the current study, the epigenetic model and role of epigenetics in development provides the molecular basis of the observations presented. The development of brain and behavior involves at least two distinct epigenetic programming mechanisms (3, 8). “Germ linedependent” epigenetic change occurs when the modified epigenome is permanently incorporated into the germ line to manifest each generation in the absence of the causative agent. “Context-dependent” epigenetic change occurs when the environmental factors that bring about the epigenetic modification persist in the environment. Most research in epigenetics today falls within this context-dependent category. Although both have been attributed with “generational” properties, only germ linedependent epigenetic modification is epigenetic transgenerational inheritance (5, 7). The life-history approach to the study of behavioral development emphasizes both the continuity and interplay between the internal and external environmental characteristic of the specific life stages. Most research on the effects of www.pnas.org/cgi/doi/10.1073/pnas.1118514109

stress has focused on the earliest life stages (fetus and neonate) or adulthood, with relatively few studies on adolescence (9–11). It is during this period that adrenarche and pubarche occur and the individual graduates from dependence to independence, assuming the properties of maturity. Stress experienced during adolescence has enduring effects, including neural remodeling, sensitivity to drugs of abuse, impaired learning and memory, and altered emotional behaviors in adulthood (12–15). The current study shows that the effects of chronic restraint stress (CRS) during adolescence on the adult physiological, behavioral, and neural phenotypes become more profound when considered in the context of epigenetic transgenerational inheritance. We investigated this complex phenotypic response with a unique statistical approach for multidimensional phenotype analysis (16). Systems biology attempts to understand how molecular- to organism-level processes are involved in the emergence of complex phenotypes. Emergence was originally formulated by Weiss (17, 18) to mean “phenotypes, and the mechanisms that underlie them, depend on, and subordinate to, the law which rules the complex as a unit.” Systems biology approaches have recently been used to examine the phenotype at the molecular level of genetics or epigenetics (19). The current study tests the hypothesis that a combination of an environmentally induced epigenetic transgenerational inheritance (lineage) and context-dependent stress (stress) interact and promote alterations in brain development and genome activity (gene networks) that alter the adult phenotype at all levels. Results In social animals, the presence of conspecifics is another powerful force shaping how an individual responds to abiotic and biotic stimuli (Fig. S1A). When housed together individuals tend to be less sensitive to stressors that, if experienced alone, are debilitating or lethal (20). Social status also influences sensitivity to negative allostatic factors, with subordinate individuals often faring more poorly than dominant individuals. Social housing also modulates both the stress response (21) and the behavior of transgenerationally epigenetically modified individuals (22). Thus, individuals from each lineage were housed together in dyads; half of the dyads were exposed to CRS.

Author contributions: D.C. and M.K.S. designed research; R.G., M.M., and M.I.S. performed research; D.C., R.G., S.V.S., M.M., M.I.S., and M.K.S. analyzed data; and D.C., R.G., S.V.S., M.M., M.I.S., and M.K.S. wrote the paper. The authors declare no conflict of interest. This article is a PNAS Direct Submission. Freely available online through the PNAS open access option. Data deposition: All microarray CEL files reported in this study have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE26737). 1

D.C. and M.K.S. contributed equally to this work.

2

To whom correspondence may be addressed. E-mail: [email protected] or skinner@ wsu.edu.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. 1073/pnas.1118514109/-/DCSupplemental.

PNAS | June 5, 2012 | vol. 109 | no. 23 | 9143–9148

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Edited by Fred H. Gage, The Salk Institute, San Diego, CA, and approved April 18, 2012 (received for review November 15, 2011)

Physiological Phenotype. Body weight (BW) and gonadosomatic and adrenosomatic indices. The pattern of BW gain differs according to

lineage and stress (Fig. S1B). There is no difference in BW between vinclozolin-lineage (V-L) and control-lineage (C-L) males at birth or at weaning. As expected, shipping stress depresses BW in all animals. The effect of lineage is observed in the nonstress groups with V-L males gaining weight more rapidly and becoming heavier than C-L males (P = 0.02). CRS depresses gain in both lineages: within 2 d of onset of CRS, weight gain (average percentage gain relative to previous weight) in stress animals is half that of nonstress males regardless of lineage; on the cessation of CRS, BW increases in both lineages. Interestingly, there is no interaction of lineage and stress. Finally, stress attenuates the difference in BW between the lineages: in the nonstress dyads, V-L males are ∼25 g heavier than C-L males are, whereas, in the stress dyads, the weight differences are less than 5 g (Fig. S1B Inset). There are no lineage effects in gonadosomatic or adrenosomatic indices, but males experiencing CRS have larger testes than do nonstress males in the V-L group and V-L stress males have larger adrenals than C-L stress males do (both P = 0.03). When considering the dyad, males in stress dyads have larger testes and adrenals (P = 0.03 and 0.02, respectively) than do males in nonstress dyads. Finally, within-dyad analysis reveals that, in the stress dyads, V-L males have larger adrenals than do C-L males (P = 0.01); this effect is not seen in nonstress dyads (Fig. S2A). Hormonal indices. With a single exception, CRS results in lower corticosterone (CORT) levels in both the C-L and V-L groups (Fig. S1C). Lineage, but not stress, influences circulating testosterone (TESTO) levels (F1, 63 = 2.11, P = 0.04). In stress animals, TESTO levels are significantly higher in V-L males relative to C-L males (P = 0.01). There is no significant difference in circulating concentrations in leptin across lineage or stress conditions, perhaps because BW is stable and unchanging by the time of death [postnatal day (PND) 120]. Behavioral Phenotype. In the forced-swim (FS) test, there is no difference according to lineage or stress condition in terms of distance, speed, latency to immobility, or time mobile measures, even after controlling for BW differences. In the open-field (OF) test, C-L nonstress males spend more time in the corners of the OF than do V-L nonstress males (Fig. 1A). Exposure to CRS has opposite effects in the two lineages (Fig. 1A): C-L males move out of corners and into the center, indicating greater exploration, whereas V-L males move from the center into corners, indicating greater anxiety [interaction between lineage and stress (F1, 56 = 3.89, P = 0.05)] (Fig. 1B). Considering the dyad, V-L males in nonstress condition cross the center more frequently (P = 0.01), whereas, in the stress condition, they cross the center faster (P = 0.04) than C-L males do. There is also an effect of stress independent of lineage: stressed males move faster through the center than do nonstressed males (P = 0.01), indicating that CRS increases anxiety later in adulthood (Fig. S2B). In sociability test 1 (Soc 1) (Fig. 1C), lineage effects are restricted to the stress dyads, with V-L males traveling farther and faster than the C-L males do (both P = 0.04) and choosing to associate with the stimulus animal more than nonstress individuals (P = 0.03). In general, CRS affects line crossing (P = 0.04) and latency to first entry into the chamber containing the stimulus animal (P = 0.01). In the nonstress dyads, V-L males visit the stimulus animal for longer periods and move between chambers less than did C-L males do (both P = 0.04) (Fig. S2B). In Soc 2, C-L nonstress males spend more time with the novel stimulus male than with the familiar stimulus male (P = 0.01) (Fig. 1 D and E). Only V-L males show effects of stress, traveling farther (P = 0.04) and faster (P = 0.05) than V-L nonstress males do; they also spend less time in the center compartment (P = 0.01) and more time with the familiar and novel stimulus males (P = 0.03). Comparison of the two tests reveals that, in Soc 1, V-L stress males tend to spend less time in the center compartment than do V-L nonstress males, a difference that becomes significant in Soc 2 (P = 0.01), suggesting that V-L 9144 | www.pnas.org/cgi/doi/10.1073/pnas.1118514109

Fig. 1. Behavior analysis. (A) In OF tests, C-L nonstress males spent more time in corners than did V-L nonstress males. (B) Heat map showing occupancy for group means in the OF from the bird’s eye view. Red indicates greater time spent at any given position. Arrows indicate change in activity as a consequence of stress. (C) Overhead view of group mean tracing of movement within a schematic of the testing chamber for animals in Soc 1. “E” indicates an empty stimulus cage; “A” indicates a stimulus cage containing an animal. (D) Overhead view of group mean tracing of movement within a schematic of the testing chamber for animals in Soc 2. “N” indicates a stimulus cage containing a novel male; “F” indicates a stimulus cage containing a familiar animal. (E) Evidence of transgenerational epigenetic modification on response to CRS on social bonding.

stress males display greater affiliation behavior with the familiar individual. In C-L males, there is no effect of stress, but mean center time decreases in Soc 2, a difference significant only in the stress condition (P = 0.03). Similarly, V-L stress males tend to spend more time in the animal chamber in Soc 1 than do V-L nonstress males and in Soc 2; this difference becomes significant (P = 0.03), again suggesting formation of a social bond with the familiar animal. See Fig. 2B and Fig. S2B for landscape analysis. Brain Metabolism Phenotype. Previous research on the neural and behavioral consequences of CRS has identified 15 brain regions that play a role in stress reactivity as well as learning and memory (Tables S1 and S2 ). Assessing metabolic activity by using cytochrome histochemistry (23) in these nuclei, we find that nine nuclei capture 87% of the variance: basolateral amygdala (BLA), medial amygdala (MeAmy), central amygdala (CeAmy), anterior cortical amygdala (CoAmy), posteromedial cortical amygdala (PMCo), medial posterior dorsal amygdala (MePD), stria terminalis (ST), Crews et al.

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Fig. 2. Phenotype analysis at different levels of biological organization. Leftmost columns depict effects of lineage (difference between C-L and V-L) under nonstress and stress conditions. An asterisk above a peak or a valley indicates a significant effect of treatment in that behavioral test (P < 0.05). Differences in phenotype calculated by permutation analysis on this dataset yielded the p results shown beneath each landscape, indicating the degree to which the landscape is changed. A peak for a trait indicates a greater result in V-L (V ) males, whereas a valley indicates a greater result in C-L (C ) males. Rightmost columns depict effects of stress (difference between nonstress and stress) in C-L and V-L males. A peak for a trait indicates a greater result in stress (S ) conditions, whereas a valley indicates a greater result in nonstress (NS ) conditions. Nodes represent group means of percentage maximum or Z scores (see SI Materials and Methods for specifics). (A) Body phenotype. Clockwise nodes: BW; ASI, adrenosomatic index; CORT; Lept, leptin level; TESTO; and GSI, gonadosomatic index. (B) Behavior phenotype. Clockwise nodes: Soc 2, measure of social novelty and working memory; OF; FS; and Soc 1, measure of social approach, anxiety, and exploration. (C) Brain metabolism phenotype. Clockwise nodes: BLA, CeAmy, MeAmy, CA1, CA3, CoAmy, PMCo, MePD, and ST. (D) Essential phenotype or the three most influential measures from each category (physiology, behavior, and brain). Clockwise nodes: TESTO, CORT, OF, Soc 1, Soc 2, MePD metabolic activity, ST metabolic activity, CA1 metabolic activity, and BW.

and CA1 and CA3 areas of the hippocampus (Table S2). V-L males subjected to CRS show an approximately 10% decrease in overall activity in the brain, but other experimental groups are relatively unchanged (Fig. 2C and Fig. S2C and Tables S1 and S2). Specific nuclei show both lineage and stress effects. The PMCo V-L males in both stress and nonstress groups show a substantial decrease (13% and 17%, respectively) in metabolic activity within the PMCo (P = 0.03,0.04, respectively) relative to C-L males. In the MeAmy, C-L stress males show an 8.4% increase in activity. In the MePD, V-L stress males show a marked decrease in activity relative to C-L stress males (∼18%, P < 0.01), whereas, in C-L stress males, there was only a 9% increase in activity. In the ST, V-L males that have been subjected to CRS show an ∼12% increase in activity relative to C-L males also subjected to CRS (P = 0.02). In V-L males, CRS results in a 10% increase in activity (P = 0.05). The CA1 and CA3 of the hippocampus show effects similar to one another. In animals that have been subjected to CRS, the CA1 shows an ∼7% decrease in activity, and the CA3 shows an 11% decrease in activity in V-L animals relative to C-L males. Similarly, in V-L animals, males that were subjected to CRS Crews et al.

show a 10% decrease in activity in the CA1 and an ∼9% decrease in activity in the CA3 relative to males that were not subjected to CRS. This effect indicates a general decrease in activity within the hippocampus in animals that have been subjected to both vinclozolin and CRS, whereas animals that were subjected to either vinclozolin or CRS (but not both) do not show great changes in activity. See Fig. S2C for landscape analysis. Essential Phenotype. An essential phenotype landscape was constructed by combining the three measures from each level of analysis that best differentiate between groups as determined by discriminant function analysis (DFA) followed by permutation analysis. This analysis determined how changes within and between phenotype classes are correlated with and separate from the effects of lineage versus the effects of CRS (Fig. 2D), revealing (i) no significant difference between C-L and V-L males; (ii) V-L males perceive and respond to CRS differently than do C-L males; and (iii) CRS affects males of both lineages to the same approximate degree, albeit it in different ways on different traits. PNAS | June 5, 2012 | vol. 109 | no. 23 | 9145

Brain Genomics and Gene Networks. For the genomic and gene network studies, RNA was derived from 1-mm punches from the CA1 and CA3 of the hippocampus, BLA, and the primary and secondary motor cortex (CRTX) from each individual (Fig. S3). The comparisons made to assess alterations in gene expression are shown in Table S3, with the C-L nonstress males considered as the baseline or “normal” brain. The number of genes with significant differences in expression with a minimum fold change of 1.2 (fold change > 1.2) and mean difference of >10 are presented for all comparisons in Table S3 and Dataset S1. The altered gene sets are each given a list number 1–16 and involve 23–377 genes, depending on the comparison and brain region analyzed. Each brain region, both within and between lineage and stress conditions, has its own set of distinct genes with negligible overlap. Indeed, only a single gene, ribosomal protein L21, is common (Fig. S4). A complete list of the genes with altered expression for each brain region and comparison is presented in Dataset S1 (lists 1–16) and categorized to various cellular functions and processes (Fig. S5), with receptors and binding proteins, metabolism, transcription, signal transduction, and development being highly represented. Various comparisons of lineage and stress conditions have genes that share common gene functional categories but are independent in their patterns of change according to lineage and stress. Analysis of the altered gene sets correlated to specific signaling pathways, and cellular processes show the top 20 pathways in multiple comparative lists (Tables S3 and S4). The highest correlated pathway is olfactory transduction, with 78 genes altered among all of the comparisons (Fig. S6). Nearly all of the comparative gene lists had the highest number of altered genes in this pathway. Other brain-related pathways affected by lineage and stress are neuroactive ligand–receptor interaction, Huntington disease, Alzheimer’s disease, axon guidance, and Parkinson disease (Tables S3 and S4). Two of the more ubiquitous pathways affected are the calcium signaling pathway and the MAPK signaling pathway (Fig. S7). Although unique gene sets exist for each brain region analyzed, the lineage and stress altered gene sets are associated with common signaling pathways and cellular processes. Interestingly, a number of brain-specific pathways associated with neurodegenerative disease were identified. The final genomic analysis of the brain region transcriptome comparisons involved identification of gene networks by using global literature analysis software with the altered brain gene sets

(24). The direct-connection (i.e., interaction) gene networks were identified for the CRTX and the CA1 regions (Fig. 3). These networks identify how the genes with altered expression are connected and associated with the changes in the brain regions and behavior. Interestingly, the two regions have distinct networks. The BLA and the CA3 have direct neural and gene network connections, and their individually identified gene networks also identify the indirectly connected genes and cellular processes they regulate. The direct-connection gene networks of the CRTX and CA1 provide novel networks of genes involved in the regulation of the brain regions and behavioral alterations. The gene networks identified involve a combination of lineage and stress factors that cannot be segregated. Similar analysis for each of the individual comparisons of lineage and stress for each region separately demonstrated no other major direct-connection gene network, but all had indirectly connected gene networks. Thus, each of the gene networks identified is unique and specific to brain region, lineage, or stress condition. Observations indicate that each brain region has a different altered gene set and gene network involved in the lineage and stress comparisons. These gene networks are directly associated with the behavioral alterations observed and are speculated to, in part, be causally related. Because neither the lineage nor the stress effects promote genetic mutations, but they do promote epigenetic alterations (7), epigenetics is the basal molecular process involved, as previously documented (6). Therefore, the germ line-dependent transgenerational modification and the context-dependent stress response modification promotes an epigenetic reprogramming of these brain regions that alters the gene networks and pathways identified to promote the altered behavioral phenotypes observed. A validation of the gene expression of the microarray data was performed with a quantitative PCR (qPCR) analysis of selected genes from the gene networks that were highly connected and critical to the regulation of the gene network. These genes were angiotensinogen (Agt) and connective tissue growth factor (Ctgf) (Fig. 3A), insulin-like growth factor binding protein 5 (Igfbp5) (Fig. 3B), and brain-derived neurotrophic factor (Bdnf) (Fig. S8A). The altered gene expression for all four genes had similar trends for the microarray and qPCR (Agt: 1.34 vs. 1.6; Ctgf: 1.31 vs. 1.92; Igfbp5: 1.70 vs. 1.36; and Bdnf: 1.21 vs. 1.63, respectively), and all had statistically significant differences (P < 0.05). Therefore, the qPCR

Fig. 3. Direct-connection networks for genes in CRTX (gene lists 5–8; A) or CA1 (gene lists 9–12; B) obtained by global literature analysis using Pathway Studio 7.0 software (Ariadne Genomics). (A) For cortex, only 22 directly connected genes of 330 unique genes (no ESTs included) from combined lists 1–4 are shown. (B) For CA1, 47 genes of 430 unique genes (no ESTs included) from combined lists 9–12 are shown. The rest of genes are not connected and not shown.

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Discussion Our observations illustrate a “two-hit” model where the “hits” span generations, in this instance the first hit (transgenerational epigenetic inheritance) predisposing a future generation to respond to a second hit (CRS during second adolescence), which further alters the adult phenotype. The first hit of this model corresponds to the exposure of a gestating female to the fungicide vinclozolin occurring three generations earlier. As demonstrated previously, vinclozolin exposure predisposes males to develop a variety of adult-onset diseases earlier than normal (5, 7), effects still detectable in males over four subsequent generations without diminution (5). These alterations in brain and behavior occur in young animals, months before the onset of these diseases (4, 22). Most research on the neural substrates of the studied behaviors has focused on the amygdala and hippocampus. Because these (and other) brain areas have glucocorticoid receptors (25), the role stress plays in plasticity in these regions has received much attention. The amygdala is an assemblage of nuclei and has no reliable structural or functional definition (26). The traditional guiding concept has been that of a “chemosensory” amygdala with its divisions based on input from the main or olfactory amygdala (for processing odor cues) versus the accessory or vomeronasal amygdala (for processing pheromonal cues). The “extended” amygdala concept relates to a functionally integrated series of nuclei (27). Regardless of the definition used, amygdaloid nuclei are involved in activation of the hypothalamo–pituitary–adrenal (HPA) axis both via their role in the control of pituitary adrenocorticotropic hormone release by stressors and the integration of behavioral responses to fear and/or anxietyprovoking conditions (28). The hippocampus both receives and sends projections to the amygdaloid nuclei, including CA1 and CA3 (29–32). Traditionally, the hippocampus is thought to inhibit stress-induced activation of the HPA (28). Although the amygdala and hippocampus tend to be studied separately for their roles in emotional behaviors and learning and memory, respectively, both structures are involved (33, 34). We find that this ancestral exposure promotes weight gain and, as such, provides pivotal empirical evidence that exposure to an endocrine disruptor in generations past results in substantial weight gain in the descendants. We also replicate the finding that this transgenerational epigenetic modification influences how individuals respond to events in their own life history (4, 22) as well as the work of others that CRS experience influences an individual’s physiological and behavioral phenotypes as an adult. CRS has an immediate and long-lasting effect on BW that correlates with CORT secretion later in life (35–38) as well as a negative relationship between stress and CORT and TESTO (39, 40). The behavioral tests measuring emotionality, anxiety, learning, and memory also reveal the well-established effects of CRS. We find a lack of effect of stress (or lineage) in the FS test (36, 41). CRS has a profound effect on the structure and function of the hippocampus (42), and, with a single exception in the CRTX, differential expression of apoptosis genes of >1.2 is restricted to the CA1 and CA3 (Fig. S3). GST (Gsp) genes are thought to be involved in stress-related oxidative damage in the pyramidal cells of the CA1 and CA3, and, in mice, CRS downregulates Gsp in these regions (43). A similar down-regulation is observed in the present study in CA1 (but not CA3) in both C-L and V-L males. Thus, for some traits, lineage and CRS have effects independent of each other. Equally important, other traits, such as circulating levels of leptin and FS, show no evidence that either epigenetic modification has an effect. Finally, the fact that C-L and V-L individuals were housed together (dyad) yet responded differently further emphasizes that the transgenerational epigenetic modification fundamentally alters how the individual responds to a common challenge. What is significant about this study is that ancestral exposure to an endocrine disruptor changes how individuals respond to CRS in Crews et al.

adolescence. Landscape analyses reveal that, depending on the phenotype, different relationships emerge. For example, at all three levels (physiological, behavioral, and brain metabolism), the effects of lineage are most apparent in the stress condition, suggesting that V-L males respond differently after CRS than do C-L males. In the physiological landscape (Fig. 2A), TESTO and CORT are mostly responsive to the effect of lineage but only in the stress condition. In both lineages, CRS slows weight gain, yet the V-L nonstress males gain weight more rapidly. The most notable effects in the behavioral landscape are the reversed effects of stress in the OF between C-L and V-L males (Fig. 2B). C-L stress males show lower anxiety, defined by fewer entries and less time in the center arena, whereas animals not exposed to CRS show elevated anxiety. This effect is reversed in the V-L animals: Stressed males show higher levels of anxiety, which is consistent with the findings of Soc 1 and 2. In the nonstress condition, V-L males show a heightened state of anxiety compared with C-L males. In C-L males, there is little effect of CRS on anxiety, as defined by the willingness to explore novel social interactions. However, in V-L males, anxiety state is decreased after CRS even beyond that displayed by C-L males. The brain metabolism landscape (Fig. 2C) shows that the amygdaloid nuclei are differentially affected by lineage. For example, cytochrome oxidase activity in PMCo is higher in C-L males regardless of stress condition. The MePD shows opposite effects after CRS (pronounced increase in C-L males and decrease in V-L males). In the MeAmy, cytochrome oxidase activity is opposite in the lineages, depending on stress. We also see that the ST, and not the bed nucleus of the ST (BnST), is markedly changed, indicating that activity in this major pathway is being modified by lineage. In CA1 and CA3, stress decreases metabolic activity in the V-L males but has no such effect in C-L males. Although the primary focus of the current study is a systems biology approach to understanding how the brain responds to ancestral exposures and environmental stress, a more targeted approach that considers specific genes can also provide insights into the general pathways and processes identified. Considering genes important in stress reactivity, V-L males have higher levels of BDNF (P = 0.03) in the BLA, whereas C-L males have higher levels of catechol-O-methyltransferase (COMT; P = 0.02) in CA1. The effects of CRS are observed in the BLA (COMT is higher in C-L nonstress males, P = 0.003) and the CA1 [melanocortin 4 receptor (Mc4r) is higher in the C-L stress group, P = 0.008]. Depending on the nucleus, gene expression can be negatively correlated: CRS in C-L animals increases expression of dopamine receptor D2 >1.5-fold in the BLA but decreases it by >1.5-fold in the CA3. The effects of the interaction of lineage and CRS are observed in the CA1 [cytochrome P450, family 19, subfamily A, polypeptide 1 (Cyp19a1) is lower in the V-L stress condition, P = 0.03], CA3 [melanocortin 3 receptor (Mc3r) and nuclear receptor subfamily 3, group C, member 1 (Nr3c1) are higher in the V-L stress group, P = 0.04 and 0.03, respectively], and CRTX [nuclear respiratory factor 1 (Nrf1) is higher in the V-L stress condition, P = 0.02]. However, in a genome-wide context, the reductionist approach and consideration of individual genes is not overly informative. Further analysis of the systems biology of these coordinated phenomena used a more extensive molecular investigation. A bioinformatics analysis of the altered brain transcriptomes revealed gene networks associated with each brain region. These regional-specific gene networks provide a molecular basis for the physiological and behavioral alterations observed. Although the gene networks were distinct, many of the altered genes in the various regions were in similar signaling pathways. For example, the olfactory transduction pathway was affected by nearly all of the lineage and stress comparisons (Tables S3 and S4 and Fig. S6). An olfactory receptor promoter has been shown to have an epigenetic transgenerational alteration in sperm (6). CRS altered 17 genes in the CA1 of V-L males and in the CRTX of C-L males. Why should genes involved in olfaction be expressed in areas of the brain not involved with olfaction and taste? Olfactory and PNAS | June 5, 2012 | vol. 109 | no. 23 | 9147

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validated the microarray data for these critical genes in the various gene networks identified.

vomeronasal receptors as a group are among the most rapidly evolving of all genes and have been linked to higher processing centers in the brain as well as to behavior (44, 45). Such findings may indicate the neurobiological and neuromolecular basis of the Proust effect, a phenomenon in which an involuntary memory reaction is triggered by an olfactory input (46). This approach also identifies brain signaling pathways associated with neurodegenerative disease (Table S4). Thus, the altered comparative gene sets and gene networks identified are anticipated to be critical in the vinclozolin lineage and stress effects on the physiological and behavioral phenotypes observed. How an ancestral environmental exposure modifies the germline epigenome and promotes epigenetic transgenerational inheritance is critical in any consideration of tissue function. 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bringing “the phenotype into being” (2) down to the molecular basis of this phenomena. Materials and Methods Detailed materials and methods and corresponding references are presented in SI Materials and Methods. In brief, two different cohorts of male rats of the F3 generation of V-L and C-L produced at Washington State University were shipped to the University of Texas at Austin on the day after weaning (Fig. S1A). Rats were randomly pair-housed (one of each lineage) and remained in these dyads throughout the duration of the study. On the day after the last behavioral test, the animals were killed by rapid decapitation, and tissue and blood samples were taken within 3 min (Fig. S9A, A and B). Brain regions were isolated, and RNA for animals from different litters was pooled to generate three different pools with the highest biological variation possible to be used in the microarray analysis. ACKNOWLEDGMENTS. We thank R. Tracey, L. Walker, D. Walker, and Y. Matsumoto for technical assistance as well as H. Johnson for assistance in preparation of the manuscript. We thank Drs. A. Gore, C. GuerreroBosagna, H. Hofmann, and M. Montfils for critical input and comments on the manuscript. This work was supported in part by National Institutes of Health Grants ES 017538 (to D.C.) and ES 012974 (to M.K.S.).

26. Swanson LW, Petrovich GD (1998) What is the amygdala? Trends Neurosci 21: 323–331. 27. Alheid GF (2003) Extended amygdala and basal forebrain. Ann N Y Acad Sci 985: 185–205. 28. Herman JP, et al. (2003) Central mechanisms of stress integration: Hierarchical circuitry controlling hypothalamo-pituitary-adrenocortical responsiveness. Front Neuroendocrinol 24(3):151–180. 29. Krettek JE, Price JL (1977) Projections from the amygdaloid complex and adjacent olfactory structures to the entorhinal cortex and to the subiculum in the rat and cat. J Comp Neurol 172:723–752. 30. Pikkarainen M, Rönkkö S, Savander V, Insausti R, Pitkänen A (1999) Projections from the lateral, basal, and accessory basal nuclei of the amygdala to the hippocampal formation in rat. J Comp Neurol 403(2):229–260. 31. Ishikawa A, Nakamura S (2006) Ventral hippocampal neurons project axons simultaneously to the medial prefrontal cortex and amygdala in the rat. J Neurophysiol 96: 2134–2138. 32. Kishi T, Tsumori T, Yokota S, Yasui Y (2006) Topographical projection from the hippocampal formation to the amygdala: A combined anterograde and retrograde tracing study in the rat. J Comp Neurol 496:349–368. 33. Packard MG, Teather LA (1998) Amygdala modulation of multiple memory systems: Hippocampus and caudate-putamen. Neurobiol Learn Mem 69(2):163–203. 34. Hale MW, et al. (2008) Exposure to an open-field arena increases c-Fos expression in a distributed anxiety-related system projecting to the basolateral amygdaloid complex. Neuroscience 155:659–672. 35. Barha CK, Brummelte S, Lieblich SE, Galea LA (2011) Chronic restraint stress in adolescence differentially influences hypothalamic-pituitary-adrenal axis function and adult hippocampal neurogenesis in male and female rats. Hippocampus 21: 1216–1227. 36. Ulloa JL, et al. (2010) Comparison of the antidepressant sertraline on differential depression-like behaviors elicited by restraint stress and repeated corticosterone administration. Pharmacol Biochem Behav 97(2):213–221. 37. Harris RB, Palmondon J, Leshin S, Flatt WP, Richard D (2006) Chronic disruption of body weight but not of stress peptides or receptors in rats exposed to repeated restraint stress. Horm Behav 49:615–625. 38. Solomon MB, Jones K, Packard BA, Herman JP (2010) The medial amygdala modulates body weight but not neuroendocrine responses to chronic stress. J Neuroendocrinol 22(1):13–23. 39. Hardy MP, et al. (2005) Stress hormone and male reproductive function. Cell Tissue Res 322(1):147–153. 40. Viau V (2002) Functional cross-talk between the hypothalamic-pituitary-gonadal and -adrenal axes. J Neuroendocrinol 14:506–513. 41. Gregus A, Wintink AJ, Davis AC, Kalynchuk LE (2005) Effect of repeated corticosterone injections and restraint stress on anxiety and depression-like behavior in male rats. Behav Brain Res 156(1):105–114. 42. Meaney MJ (2001) Maternal care, gene expression, and the transmission of individual differences in stress reactivity across generations. Annu Rev Neurosci 24:1161–1192. 43. Ejchel-Cohen TF, et al. (2006) Chronic restraint stress decreases the expression of glutathione S-transferase pi2 in the mouse hippocampus. Brain Res 1090(1):156–162. 44. Feldmesser E, et al. (2006) Widespread ectopic expression of olfactory receptor genes. BMC Genomics 7:121. 45. Dulac C, Wagner S (2006) Genetic analysis of brain circuits underlying pheromone signaling. Annu Rev Genet 40:449–467. 46. Chu S, Downes JJ (2000) Odour-evoked autobiographical memories: Psychological investigations of Proustian phenomena. Chem Senses 25(1):111–116.

Crews et al.

Supporting Information Crews et al. 10.1073/pnas.1118514109 SI Materials and Methods Animal Housing Protocol. F3 generation vinclozolin-lineage (V-L) and DMSO control-lineage (C-L) male rats were selected out of litters from untreated F2 generation mothers in M.K.S.’s laboratory at Washington State University (WSU) according to established protocols (1). Briefly, approximately four different F0 generation females were used to generate different lineages for the F1–F3 generations with no sibling or cousin breeding to avoid inbreeding artifacts. Gestating female F0 generation Sprague–Dawley rats were injected with the fungicide vinclozolin (100 mg/kg) daily during fetal gonadal sex determination (embryonic days 8–14), and the F1 generation were bred to generate the F2 generation, and then the F2 were bred to generate the F3 generation (1). At approximately postnatal day (PND) 10 (before weaning), each animal was injected with a small microchip (AVID) s.c. between the shoulder blades. The animals were then shipped to D.C.’s laboratory at the University of Texas at Austin (UTA) from WSU on PND 22, 1 d after weaning. Upon arrival at the UTA, one animal from each lineage (control and vinclozolin) was pairhoused (one control and one vinclozolin animal) and remained in these dyads throughout the duration of the study. Because of the natural variation in dates of breeding, there was a 4-d spread of birth date of animals in the first cohort, but all animals were born on the same day in the second cohort. However, all pair-housed animals were no more than 1 d apart in birth age and were paired randomly to prevent an age effect on cage mates. Each dyad of animals was randomly placed in a six-wide, fivehigh metal housing rack in standard translucent polycarbonate rat cages (46 cm × 24 cm × 20.5 cm) with ad libitum access to tap water and standard rat chow (rodent chow 5LL2 Prolab RMH 1800 diet; Purina). The animal room was on a 14-h/10-h light/ dark schedule. For environmental enrichment, a 7-cm-diameter PVC pipe was placed in each cage. Uterine and litter sex ratios can influence adult phenotype (2– 4), and so the sex ratio of each litter was determined at birth and weaning. The litters were then divided according to criteria described in de Medeiros et al. (4). Equal (E) litters (n = 5 litters totaling 20 animals) containing equal numbers of males and females (or no more than 1 individual more of either sex). Malebiased (Mb) litters (n = 5; 23 animals) contained ≥50% males. Female-biased (Fb) litters (n = 9; 42 animals) contained ≥50% females. All of the litters that provided animals in the study could be divided into one of these three groups. Chronic Restraint Stress (CRS). The day after receipt at UTA, half of the dyads were randomly chosen to be administered a CRS treatment. This paradigm entailed 6 h of daily CRS consecutively for 21 d and duplicated the methodology of ref. 5. The restraint apparatus consisted of a 25.4-cm2 metal wire mesh folded in half and bound with a plastic mold that allowed for two openings and prevented any rough edges. The front and rear openings of the restraint cage were clipped shut with binder clips with an additional binder clip on one side of the animal to allow for adjustment of the size of the restraint as the animals grew. Animals to be stressed were removed from the animal housing room at 9:00 AM and transported to a procedural room separate from the housing room. Each animal was hand-placed in a restraint at 1 h after lights off (9:30 AM) by either allowing the animal to enter the restraint on its own will or gently coaxing the animal into the restraint. Extra care was taken to not forcefully place the animals in the restraint as to prevent any unnecessary stress. Stressing was performed between 9:30 AM and 3:30 PM, with lights off Crews et al. www.pnas.org/cgi/content/short/1118514109

and no red light. At 3:30 PM, animals were immediately removed from the restraint cages by removing the binder clip closest to the animal’s nose, allowing them to crawl out of the restraint into their home cage at will. As each animal was placed back in its home cage, it was scanned to confirm identity and correct cage mate placement. The animals were then transported back to the housing room and placed back in their original housing rack. Dyads that were not to be stressed were left in the housing room, untouched. Restraint cages and binder clips were washed after stressing each day with soap and water and left to dry for the next day’s stressing. Twice a week (Tuesday and Friday), after the animals had been stressed, animals were weighed, beginning at 4:00 PM. While each dyad was being weighed, the animals were handled for about 3 min each to allow the animal to become accustomed with the experimenter and to prevent any unnecessary stress while the animals had to be handled for stressing or behavioral testing. After the initial 21 d of CRS, all animals were left in the housing room constantly and were only removed for handling, weighing, and behavioral testing on scheduled days. Animal Groups and Numbers. There were four treatment groups: V-L stress (VS), V-L nonstress (VNS), C-L stress (CS), and C-L nonstress (CNS). A subset of each group was not tested (4, 2, 4, and 2, respectively); all remaining dyads were behaviorally tested. Two cohorts of animals were run, the first in January and the second in May. Cohort sample sizes are shown in the following table:

Cohort 1 2 Total

CNS

VNS

CS

VS

8 8 16

8 8 16

11 9 20

10 9 19

Body Weight (BW). Animals were weighed every 3–8 d from PND 21 (at weaning) to PND 108. Analysis focused on two questions: how do the groups differ through time or at any one point in time and how does weight change within a group as a function of time and experience. The first question was addressed by using a three-way ANOVA with repeated measures. The second question was addressed in the following manner. Differences in BW between a stress group and a nonstress group and between V-L and C-L were compared at each time point (PNDs 21, 29, 32, 37, 40, 46, 52, 57, 61, 67, 71, 79, 81, 88, 96, 102, and 108). The effect of CRS on BW was compared between and within lineages at each time point. The nonparametric Wilcoxon rank-sum test was used to analyze the association between a lineage and stress treatment because of the asymmetric distribution of BW in each group. All statistical comparison was performed with JMP 8.0 (SAS Institute); P values < 0.05 were considered to be statistically significant. Behavioral Testing. Beginning at PND 114, each individual received four different behavioral tests with behavior quantified by using the automated Stoelting ANY-maze video-tracking system. Each test was separated by 48 h. All of the dyads (V-L and its yoked C-L cage mate) were tested in open-field (OF), forced-swim (FS), and two social-affiliation tests. The order of the tests was counterbalanced to treatment, although the OF test was obligatory to the last day of 1 of 17

testing because it was performed during the light phase to control for the time between tests. Animals were then killed 42 h later. After each trial, the apparatus was cleaned with 70% (vol) ethanol and allowed to dry before the next test. The FS and sociability tests were performed during the dark cycle, beginning at 1 h after lights off (9:30 AM). The test arenas were softly illuminated with red lights, positioned as to not affect ANY-maze tracking. The OF was performed during the light cycle under illumination, beginning at 1 h after lights on (7:30 PM). To prevent ambiguities in testing each animal, a scanning system was used that automatically scanned the identity of the animal, via an AVID identification microchip, that was automatically entered into ANY-maze and began each test. FS test. This test was based on the methods of Porsolt et al. (6). However, because there was no intermittent treatment to administer, a single 15-min paradigm was used. Animals were placed in a 19 cm × 50 cm Plexiglas cylinder with 40 cm of water. Each animal was allowed 15 min in the cylinder with no possibility of escape (a piece of clear glass was placed over each apparatus to prevent escape). The ANY-maze system was then instructed to measure the time that each animal was immobile, defined as no more movement than necessary to keep the head above the water to breathe. The depth of the water was such that an animal would not be able to balance itself on the bottom of the tank with its tail. If an animal sank to the bottom of the tank and exhaled their breath under water, they were immediately removed from the tank and scored as a “did not finish.” Water for the FS was tap water that had been placed in containers overnight to allow the temperature of the water to come up to room temperature (23–25 °C). After each trial, the water was poured out and the cylinder was rinsed with water, rinsed with 70% ethanol, rinsed with water again, and then filled with room temperature water. After each trial, each animal was hand-dried with a towel and placed back into its cage with a red light directly above the cage for warming the animal from hypothermia. OF test. Each animal was tested in a 100 cm × 100 cm × 40 cm apparatus partitioned into four equivalent arenas of 50 cm × 50 cm each). A soft white light bulb (60 W) was placed directly over the enclosure. No other ambient lights were on during testing. Each animal was placed at the corner where the partition met (i.e., in the center of the 100 cm × 100 cm arena) to rule out initial placement of the animal in the arena as a factor affecting behavior. The animal was then allowed a 15-min period to roam the arena with no interruption. A 10-cm perimeter border around the edges of the arena was drawn digitally in ANY-maze and defined as an “outer region,” and anything inside of that 10-cm border was defined as the “inner region.” ANY-maze was instructed to calculate the time in the inner region versus the time in the outer region as well as the following measures: total distance traveled (m), average speed (m/s), number of line crossings, time in inside zone (s), number of entries into the outside zone, and time in outside zone (s). To obtain a measure of time spent in corners, the OF was divided into 25 equal segments, and the four corner segments were summed. After the 15-min trial period, each animal was removed and returned to its home cage. The arena floor and walls were cleaned with 70% ethanol and left to air-dry before the beginning of the next trial. Tests for sociability. Two tests for sociability were modeled after protocols in Moy et al. (7). A 100 cm × 100 cm × 40 cm Plexiglas enclosure (Stoelting) was partitioned into three arenas by 40-cm high walls with a 10 cm × 11 cm opening to allow movement of the rat between arenas. At the beginning of the test, the animal was allowed to become accustomed to its environment for 5 min. The center arena was used for this, and the entrances to the two side arenas were blocked by standard poster board taped to the wall of the arena. A 5-min habituation period preceded each test. All stimulus animals were PND 120 intact Sprague–Dawley male rats from Harlan. The stimulus animal cage was a 15 cm × 30 cm enCrews et al. www.pnas.org/cgi/content/short/1118514109

closure with vertical rods spaced at 1 cm apart to prevent fighting and biting but allowing for facial recognition and investigation. For sociability test 1 (Soc 1), the blockades to the two side chambers were removed after the habituation period, allowing the experimental rat to explore any of the three chambers. The position (left or right) of the stimulus animal was systematically rotated between trials. The experimental rat was given 10 min to become familiar with the stimulus animal. ANY-maze was instructed to record the time spent in the chamber with animal 1 versus the center and other chambers (containing an empty cage). In Soc 2, a second stimulus animal (novel animal), pair-housed with the first animal (familiar animal) was placed in the empty cage in the opposite chamber. The experimental rat then had the choice of associating with the familiar rat or with the novel rat or not associating with either. ANY-maze was instructed to record the time spent with the novel animal versus the time spent with the familiar animal versus the time spent in the center arena (no animal). After this second 10-min period, the rat being tested was returned to its home cage, and the arena and metal enclosures were wiped down with 70% ethanol and allowed to air-dry. Hormone Assays. The hormone RIAs were performed by the Hormone Assay Core Laboratory at the Center for Reproductive Biology, WSU. Circulating concentrations of corticosterone (CORT), testosterone (TESTO), and leptin were determined by commercial assays (TESTO and CORT from Siemens Medical Solutions with coefficients of variation at less than 6.18% and 6.7%, respectively). Each cohort was analyzed in separate assays for TESTO and CORT, with the latter hormone conducted in a single assay. The leptin commercial assay was from Millipore with a coefficient of variance less than 7.3%. Brain Processing. For each dyad, the brain of each male was cut in the sagittal plane at the midline (Fig. S8A, A–D). Each half was combined with the complementary half of the other individual (alternating the right and left halves) such that each “brain” consisted of symmetrical halves of the V-L and a C-L male pair. One “combined” brain was prepared for cryostat sections (40 μm) in three alternating sets: the first set was for cytochrome oxidase histochemistry (8) and the second and third sets were kept for future studies, such as in situ hybridization and immunohistochemistry of target genes for better resolution of gene expression. The other combined brain was prepared for punches of discrete nuclei by first slicing in 2-mm sections with a Zivic brain matrix (Fig. S8A, E–G. The following coordinates are relative to bregma based on the Paxinos and Watson (9) rat brain atlas: the beginning of each blocked slice was +0.36, −1.64, −3.64, and −5.64. The following areas were taken using a 1-mm punch (Stoelting): primary and secondary motor cortex (CRTX) at the level of the basolateral amygdala (BLA), BLA, and CA1 and CA3 of the hippocampus. Tissue punches were placed singly in 1-mL Eppendorf tubes containing 200 μL of TRIzol. All brain analyses (microarray and cytochrome oxidase histochemistry) were conducted after all tissues had been collected so that material from all individuals could be done in a single run for each procedure. Cytochrome Oxidase and Brain Nuclei. Behavior is a function of brain activity, which obtains ∼90% of its energy from the aerobic metabolism of glucose (8). Cytochrome oxidase (COX) is a ratelimiting enzyme in oxidative phosphorylation. COX activity reflects the metabolic history of brain areas, and COX levels and/ or activity constrain the activity of a neuron, thereby limiting the likelihood of a behavior (10). Thus, factors that constrain brain metabolism also constrain behavior. Considering that behavior results from coordinated activity in networks of specific brain nuclei (11), information on the metabolic activity in neural networks is of interest. 2 of 17

Metabolism is assessed by cytochrome oxidase histochemistry in 14 discrete brain regions (Tables S1 and S2): All regions but the CRTX have been implicated in the neural and behavioral consequences of response to CRS. The primary disadvantage of the split-brain method is that midline nuclei such as the paraventricular nucleus (PVN) and anteroventral periventricular nucleus (AvPv) are damaged and in most instances cannot be imaged with confidence. For example, the PVN is integral to the stress response (12). Although we were able to obtain total metabolic measurements for the PVN, the sample sizes were limited (two or more per group). The PVN in C-L males had substantially higher activity (>35%) than V-L males in the nonstress condition (P = 0.02); this effect was reduced to ∼10% difference in the stress condition. Only the C-L males showed a response to CRS (32% decrease; P < 0.01), whereas the V-L males showed an approximately 10% change in the stress condition. Landscape Analysis. The functional landscape analysis developed involves principal component analysis (PCA) followed by discriminant function analysis (DFA) and permutation analysis to determine whether the targeted traits at each level of biological organization (physiology, behavior, and brain nuclei metabolism) are different between groups (11, 13). Performing a traditional PCA requires either omitting individuals with missing data points or imputing the missing data. We opted for an alternative method for PCA termed probabilistic PCA (PPCA), capable of accommodating missing data (13). Before the analysis, individuals with greater than 50% of their data missing were removed (n = 5 individuals), and the data were recentered to mean 0 and scaled via vector normalization. The remaining missing data were imputed during PPCA (n = 36 data points) (14). Unlike traditional PCA, PPCA can handle missing data (14). In PPCA, an expectation-maximization algorithm is used to fit a Gaussian latent-variable model (14). The maximum-likelihood estimate for the missing data was determined from the observed conditional distributions for individuals with complete data (13, 14). All data-preprocessing and PCA were carried out using the MultiDimBio (13) R package (v0.0.2) and bioconductor (release 2.8) R package pcaMethods (v1.32.0) (15). The imputed data account for 6% of the total dataset. A multivariate ANOVA (MANOVA) was conducted on the results of the PPCA. Lineage, stress, their interaction, and housing dyad were included in the model. The interaction between dyad and the other group variables was not modeled because the effect of dyad should be random with respect to lineage and stress. The number of unique housing dyads also preclude this analysis because there are not enough degrees of freedom. Post hoc analysis was carried out with four ANOVAs, one for each principal component axis. Significance was determined by using a false discovery rate correction as implemented in the R package fdrtools (16). All analyses were performed with R v2.12.2 (17). The effects of lineage and stress on the physiological, behavioral, brain metabolism, and essential phenotypes were analyzed (Fig. 2 A–D, respectively). PCA was performed on six measures of body phenotype: leptin level, TESTO level, CORT level, adrenal weight, testes weight, and animal BW. The first four principal components were maintained and account for 81% of the variance (Fig. S2A). The first and second principal components (PC1 and PC2) were organ/animal weight and circulating hormones, respectively. The third principal component (PC3) was dominated by leptin levels, and the fourth principal component (PC4) related adrenal size to CORT levels. A MANOVA of the principal component scores for effects of lineage, stress, and dyad revealed a significant effect of lineage (F1, 32 = 4.49, P = 0.006), stress (F1, 32 = 4.00, P = 0.011), and dyad (F34, 32 = 4.49, P = 0.006) but no significant interaction. The individual importance of each axis was explored post hoc by using Crews et al. www.pnas.org/cgi/content/short/1118514109

four separate ANOVAs. There was a significant effect of lineage in PC1 and PC3 (F1, 32 = 7.54, qFDR = 0.02; F1, 32 = 7.31, qFDR = 0.021), stress in PC1 (F1, 32 = 17.88, qFDR = 0.002), and dyad in PC2 and PC4 (F34, 32 = 2.59, qFDR = 0.013; F34, 32 = 7.31, qFDR = 0.008), where qFDR is the false discovery rate q value. PCA of the combined behavioral tests revealed that the first three principal components account for 93% of the variance (Fig. S2B). A MANOVA of the principal component scores for effects of lineage, stress, and dyad revealed no significant effects variation. The individual importance of each axis was explored post hoc by using four separate ANOVAs, again with no statistically significant effects of lineage, stress, dyad, or their interactions. PCA of the essential phenotype captured 69% of the variance observed among and between the groups. PCA revealed that nine brain nuclei capture 87% of the variance: BLA, medial amygdala (MeAmy), central amygdala (CeAmy), anterior cortical amygdala (CoAmy), posteromedial cortical amygdala (PMCo), medial posterior dorsal amygdala (MePD), stria terminalis (ST), and CA1 and CA3 of the hippocampus. The first four principal component axes account for >92% of the variation. The first principal component likely represents a measure of general activity in the sampled brain regions, with all nuclei except ST strongly loading onto the axis (Fig. S2C). The second axis is dominated by CA1 and CA2, and the third axis is almost entirely determined by ST. The fourth axis accounts for slightly more than 5% of the variation and is strongly determined by PMCo and, to a lesser extent, CA1, CA3, and CoAmy. To test for the effect of lineage, stress, and their interaction, we used the principal component scores as response variables in a MANOVA. Housing dyad (dyad) is also included as a covariate. There is a significant effect of lineage (F1, 29 = 8.99, P < 0.001) and dyad (F1, 29 = 3.14, P < 0.001), a trend toward a significant interaction (F1, 29 = 2.56, P = 0.063), and a nonsignificant effect of CRS. The individual importance of each axis is explored post hoc by using four ANOVAs. The overall result is a strong effect of vinclozolin on the response to CRS. The first and fourth principal component axes contribute to lineage (F1, 29 = 6.55, P = 0.028; F1, 29 = 8.60, P = 0.021) and dyad effects (F1, 29 = 4.04, P = 0.001; F1, 29 = 2.35, P = 0.024). The third principal component accounts for the interaction between lineage and CRS (F1, 29 = 4.64, qFDR = 0.055), and the second principal component only contributes to the effect of dyad (F1, 29 = 2.48, qFDR = 0.022). There is a significant effect of dyad in the MANOVA and all ANOVAs, except for the PC3 ANOVA. RNA Preparation. From each individual, 1-mm punches were taken from the CA1 and CA3 of the hippocampus, the BLA, and the CRTX. After RNA isolation, three different pools, each containing three different males, were generated in each of the four conditions. Microarray analysis was performed on each pool in triplicate, involving three different experiments and aged animal pools. The sample histograms for raw data for all 48 arrays are shown in Fig. S3 and after preprocessing (,SI Materials and Methods) all arrays corresponded well with no outlying arrays. Individual rats were homogenized in 200 μL of TRIzol, and then 600 μL of TRIzol was added to final volume of 800 μL. Samples were stored at −80 °C or −20 °C until RNA extraction. Then, 100 μL of the above TRIzol homogenate from four randomly chosen individuals within the same tissue/treatment group were pooled together for one RNA sample (one microarray biological replica). Samples from the same set of four dyads were pooled for one vinclozolin or control replica for all four brain areas, stress or nonstress. For microarray analysis, three biological replicas were prepared as above for each brain area/treatment group. A total of 48 samples/chips were analyzed: 4 (brain areas) Χ 2 (control or vinclozolin) Χ 2 (stress or nonstress) Χ 3 (biological replicas). RNA was extracted from pooled TRIzol samples according to 3 of 17

Other Statistical Analysis. All measures for behavioral analysis were acquired automatically from the ANY-maze behavioral tracking program (Stoelting). Visual confirmation of the system was performed as each animal was tested to ensure accuracy. All behavioral measures were formatted for use in SPSS to perform statistical analyses in two basic variations, parametric and nonparametric. Several parametric statistics were used. For the behavioral tests, a two-way ANOVA (stress × lineage) was performed on each of the measures obtained from ANYmaze looking for main effects of stress, main effects of lineage, and interactions as well as for each Hochberg’s GT2 post hoc analysis applied. Significance was determined at α < 0.05. Additionally, t tests were performed on a 2 × 2 design looking for stress effects within lineage (i.e., C-L nonstress condition versus

C-L stress condition or V-L nonstress condition versus V-L stress condition) or lineage effects within stress (i.e., V-L stress condition versus C-L stress condition or V-L nonstress condition versus C-L nonstress condition). t test statistics are indicated as being either one- or two-tailed analyses depending on a priori hypotheses of each of the measures. That is, if directionality was hypothesized, statistics are displayed as one-tailed analyses with a significance α = 0.05. To clarify social interactions and rule out the confounding effects of differences between cage mates (social context), statistics were performed on a matched-pair basis. As previously described, animals were pair-housed with an animal of the other lineage (C-L with V-L). The value of each measure for each C-L animal was subtracted from the measure for its V-L cage mate, creating a difference score for each measure. Because the resulting scores were not normally distributed, based on the Kolmogorov–Smirnov test for normality, they were compared with nonparametric statistics. To compare the effects of CRS between dyads, the same difference scores described above were compared with a Kruskal–Wallis one-way ANOVA. To determine an effect of lineage within each dyad, a pair-matched signed-rank Wilcoxon test was performed. In all these tests, statistical significance was P < 0.05. In addition to traditional comparisons, a combined Z score of multiple measures was composed for each behavioral test based on the work of Bellani et al. (20). Each measure was prechosen as a measure of anxiety or sociability whereupon it was transformed to a Z value. These Z values were then summed for each animal within each behavioral test. These sum scores of Z values were then compared in a two-way ANOVA and by t tests, as described above. The combined and averaged Z scores for each group were plotted onto a surface map to create a behavioral phenotype of that group. To determine the change in a phenotype relative to a stress or lineage condition, surface plots were subtracted across lineage or stress, but not both, to elucidate those effects (Z2–Z1). All significance levels were restricted to α = 0.05. At death, each animal’s adrenals and testes were removed and weighed for analysis. The weights of these organs were compared as whole weights and as an index to BW, thus controlling for total size of the animal. As with the statistical analyses on behavioral measures, organ weight data were parsed into their respective groups and compared via a two-way ANOVA and t tests. The same interdyad comparison described above was used to determine any effects of social context. All significance levels were restricted to α = 0.05. Hormone assays were performed at WSU, and subsequent statistical analyses were performed at UTA. CORT, TESTO, and leptin were measured by RIA and were compared both directly and as an index of organ weight (e.g., TESTO to testes weight). As with the statistical analyses on behavioral measures, hormone data were parsed into their respective groups and compared via a twoway ANOVA and t tests. The same interdyad comparison described above was used to determine any effects of social context. All significance levels were restricted to α = 0.05. In the instance of CORT levels, there appeared to be an effect of litter sex ratio. Although the litter sex ratio of the V-L and C-L does not differ in the colony at large, post hoc analysis of the data revealed that males from equal and female-biased litters exhibit a significant decline (averaging 39%) in CORT levels as a consequence of CRS in both C-L and V-L groups, whereas males from male-biased litters exhibit a significant elevation (31%) in CORT levels. There is no effect of litter sex ratio for either TESTO or leptin.

1. Anway MD, Cupp AS, Uzumcu M, Skinner MK (2005) Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science 308:1466–1469.

2. Crews D, Fuller T, Mirasol EG, Pfaff DW, Ogawa S (2004) Postnatal environment affects behavior of adult transgenic mice. Exp Biol Med (Maywood) 229:935–939.

standard TRIzol extraction protocols (Invitrogen) and stored in aqueous solution at −80 °C until microarray analysis. Microarray Analysis. The microarray analysis was performed by the Genomics Core Laboratory at the Center for Reproductive Biology, WSU, by using standard Affymetrix reagents and protocol. Briefly, mRNA was transcribed into cDNA with random primers, cRNA was transcribed, and single-stranded sense DNA was synthesized, fragmented, and labeled with biotin. Biotin-labeled ssDNA was then hybridized to the Rat Gene 1.0 ST microarrays containing more than 29,000 transcripts (Affymetrix). Hybridized chips were scanned on an Affymetrix Scanner 3000. CEL files containing raw data were then preprocessed and analyzed with Partek Genomic Suite 6.5 software using an RMA GC content-adjusted algorithm. Raw data preprocessing was performed in four groups, one for each of four brain areas (BLA, CRTX, CA1, and CA3; Fig. S4 B, C, E, and F). Comparison of raw data array histogram graphs for each brain tissue demonstrated the data for all 12 chips belonging to one of four tissues were similar and appropriate for further preprocessing and analysis as a whole group (Fig. S4 A and D). Preprocessing of raw data involved multiple testing corrections and false discovery rate corrections (18). The microarray quantitative data involves hybridization signals from an average of 28 different oligonucleotides arrayed for each gene, and the hybridization must be consistent to allow a statistically significant quantitative measure of gene expression and regulation. In contrast, a quantitative PCR (qPCR) procedure only uses two oligonucleotides, and primer bias is a major factor in this type of analysis. Therefore, we did not attempt to use PCR-based approaches for gene expression measurement because we feel the microarray analysis is more accurate and reproducible without the primer bias found in PCR-based approaches, as previously described (18). All microarray CEL files from this study have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm. nih.gov/geo (accession no. GSE26737), all arrays combined with one accession number. For gene annotation, Affymetrix annotation file RaGene1_0stv1.na31.rn4.transcript.csv was used unless otherwise specified. Gene Network and Pathways. Global literature analysis of differentially expressed gene lists for each tissue or treatment group was performed by using Pathway Studio software (Ariadne Genomics), which performs an interaction analysis and builds subnetworks of genes and cell processes connected to each other. Resulting lists of differentially expressed genes for each treatment and each tissue were analyzed for KEGG (Kyoto Encyclopedia of Genes and Genomes, Kyoto University, Japan) pathway enrichment with Pathway-Express, a web-based tool freely available as part of the Onto-Tools (http://vortex.cs.wayne.edu) (19), and the Search Pathway tool at http://www.genome.jp/kegg/pathway.html.

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3. Crews D, Rushworth D, Gonzalez-Lima F, Ogawa S (2009) Litter environment affects agonistic behavior and brain metabolic activity of adult estrogen receptor α knockout mice. Frontiers in Behavioral Neuroscience 3:12. 4. de Medeiros CB, Rees SL, Llinas M, Fleming AS, Crews D (2010) Deconstructing early life experiences: Distinguishing the contributions of prenatal and postnatal factors to adult male sexual behavior in the rat. Psychol Sci 21:1494–1501. 5. Romeo RD, Bellani R, McEwen BS (2005) Stress-induced progesterone secretion and progesterone receptor immunoreactivity in the paraventricular nucleus are modulated by pubertal development in male rats. Stress 8(4):265–271. 6. Porsolt RD, Le Pichon M, Jalfre M (1977) Depression: A new animal model sensitive to antidepressant treatments. Nature 266:730–732. 7. Moy SS, et al. (2004) Sociability and preference for social novelty in five inbred strains: An approach to assess autistic-like behavior in mice. Genes Brain Behav 3(5):287–302. 8. Gonzalez-Lima F, Cada A (1998) Quantitative histochemistry of cytochrome oxidase activity. Cytochrome Oxidase in Neuronal Metabolism and Alzheimer’s Disease, ed Lima FG (Plenum, New York), pp 55–90. 9. Paxinos G, Watson C (2007) The Rat Brain in Stereotaxic Coordinates (Academic, New York). 10. Sakata JT, Crews D, Gonzalez-Lima F (2005) Behavioral correlates of differences in neural metabolic capacity. Brain Res Brain Res Rev 48(1):1–15. 11. Crews D, Lou W, Fleming A, Ogawa S (2006) From gene networks underlying sex determination and gonadal differentiation to the development of neural networks regulating sociosexual behavior. Brain Res 1126(1):109–121.

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12. Herman JP, Flak J, Jankord R (2008) Chronic stress plasticity in the hypothalamic paraventricular nucleus. Prog Brain Res 170:353–364. 13. Scarpino S, Gillette R, Crews D (2012) MultiDimBio: An R package for the functional landscape analysis of multivariate data. J Stat Softw, in press. 14. Tipping ME, Bishop CM (1999) Probabilistic principal component analysis. J R Statist Soc B 61:611–622. 15. Stacklies W, Redestig H, Scholz M, Walther D, Selbig J (2007) pcaMethods— a bioconductor package providing PCA methods for incomplete data. Bioinformatics 23:1164–1167. 16. Strimmer K (2008) fdrtool: A versatile R package for estimating local and tail areabased false discovery rates. Bioinformatics 24:1461–1462. 17. R Development Core Team (2011) R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, Austria). 18. Nilsson EE, et al. (2010) Gene bionetwork analysis of ovarian primordial follicle development. PLoS ONE 5:e11637. 19. Draghici S, et al. (2007) A systems biology approach for pathway level analysis. Genome Res 17:1537–1545. 20. Bellani R, Luecken LJ, Conrad CD, Conrad CD (2006) Peripubertal anxiety profile can predict predisposition to spatial memory impairments following chronic stress. Behav Brain Res 166(2):263–270.

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Fig. S1. Experimental design and phenotypic analysis. (A) Paradigm to test the interaction of germ line-dependent (V-L) and context-dependent (CRS during adolescence) epigenetic effects on morphology, physiology, behavior, metabolism, and gene networks in the brain. Individual male rats were weaned at PND 21 and then shipped from WSU to UTA. On receipt, each V-L male was paired with a vehicle C-L male and housed together thereafter. On the day after receipt, half of the pairs were subjected to a regimen of CRS daily for 6 h for 21 d, whereas the other half of the pairs were not stressed. (B) Effects of germ linedependent (V-L) and context-dependent (stress) epigenetic modifications on BW. Animals were weighed at weaning (PND 21) at WSU and again on receipt at UTA (PND 25). Illustrated is group mean BW (g) ± SEM. Purple, C-L nonstress condition; blue, V-L nonstress condition; yellow, C-L stress condition; and red, V-L stress condition. BW in each group was also compared. C-L stress condition and V-L stress condition are significantly lower than C-L nonstress condition at PND 29 (P = 0.003 and P = 0.012, respectively), PND 32 (P < 0.001 for both), PND 37 (P < 0.001 for both), PND 40 (P < 0.001 for both), PND 46 (P = 0.007 and P = 0.008, respectively), and PND 52 (P = 0.016 and P = 0.003, respectively). At PND 57 only, C-L stress group has a lower BW than C-L nonstress group (P = 0.009). V-L nonstress condition had a significantly higher BW than C-L nonstress condition at PND 46 (P = 0.048), PND 52 (P = 0.013), PND 61 (P = 0.021), and PND 67 (P = 0.046). In the nonstress groups, the V-L males had higher BW than did C-L at PND 52 (P = 0.026) and PND 96 (P = 0.046). There was no significant BW difference between the C-L stress condition and V-L stress condition males. In C-L, CRS had a significant effect on BW at PND 29 (P = 0.002), PND 32.5 (P < 0.002), PND 37 (P < 0.001), PND 40 (P < 0.001), PND 46 (P = 0.003), PND 52 (P = 0.003), PND 57 (P = 0.003), PND 61 (P = 0.028), and PND 67 (P = 0.03). In the nonstress groups, V-L males tend to have a higher BW than C-L males do at PND 52 and PND 96. However, this lineage-specific BW difference was not seen in stress groups. CRS resulted in a decrease in BW in both lineages. This effect diminished after animals had recovered from the CRS treatment (PND 67) in the C-L males. However, Legend continued on following page

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BW in the stress condition continued to be lower than in the nonstress condition in the V-L animals. Exposure to CRS did not seem to have differential effect between two lineages; however, it had a significant effect within a lineage, particularly in V-L males. In these males, the decrease in BW because of the CRS lasted longer than in the C-L males. Therefore, the transgenerational influence of vinclozolin does not affect BW in a synergistic fashion with exposure to CRS; rather, it changes sensitivity toward to external stress during this important life-history stage. (Inset) Graph shows the moving average (n = 3 consecutive weighings) of weight differences within each dyad for stress (red) and nonstress (blue) (V-L minus C-L). (C) Circulating concentrations of CORT and TESTO in V-L and C-L males that received CRS (gray bars). Comparison is with males that did not receive CRS (white bars).

Fig. S2.

(Continued)

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Fig. S2.

(Continued)

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Fig. S2. Phenotype analysis. (A) Relative importance for each physiological trait (leptin, TESTO, CORT, adrenal weight, testes weight, and BW) across the four principal component axes. On the left are the four principal component axes (PC1–PC4). The loading score for each nuclei is transformed into the relative weight by taking the absolute value and dividing by the sum of the loadings across all nuclei. A value of 1 indicates that the axis is entirely determined by that nucleus, whereas a value of 0 indicates that nucleus contributes no information to that axis. On the right are the interaction plots for each principal component axis. NS, not significant. PC1: stress (F = 17.8816, P < 0.001, qFDR = 0.002), lineage (F = 7.5362, P = 0.001, qFDR = 0.019), interaction (NS). PC2: stress (NS), lineage (NS), interaction (NS). PC3: stress (NS), lineage (F = 7.3091, P = 0.01, qFDR = 0.021), interaction (NS). PC4: stress (NS), lineage (NS), interaction (NS). Significance for both main effects and interactions were determined by using ANOVAs and a false discovery rate correction (with qFDR < 0.05 being significant). (B) Relative importance for each behavioral trait (FS, OF, Soc 1, and Soc 2) across the three principal component axes. On the left are the three principal component axes (PC1–PC3). The loading score for each nuclei is transformed into the relative weight by taking the absolute value and dividing by the sum of the loadings across all nuclei. A value of 1 indicates that the axis is entirely determined by that nucleus, whereas a value of 0 indicates that nucleus contributes no information to that axis. On the right are the interaction plots for each principal component axis. NS, not significant. PC1: stress (NS), lineage (NS), interaction (NS). PC2: stress (NS), lineage (NS), interaction (NS). PC3: stress (NS), lineage (NS), interaction (NS). Significance for both main effects and interactions were determined by using ANOVAs and a false discovery rate correction (with qFDR < 0.05 being significant). (C) Relative importance for metabolic activity in each brain nucleus (BLA, MeAmy, CeAmy, CoAmy, PMCo, CA1, CA3, MePD, and ST) measured across the first four principal component axes. On the left are the four principal component axes (PC1–PC4). The loading score for each nuclei is transformed into the relative weight by taking the absolute value and dividing by the sum of the loadings across all nuclei. A value of 1 indicates that the axis is entirely determined by that nucleus, whereas a value of 0 indicates that nucleus contributes no information to that axis. On the right are the interaction plots for each principal component axis. An interaction plot represents the effect of treatment and stress for each of the four axes. NS, not significant. PC1; stress, (NS), lineage (F = 6.545, P = 0.016, qFDR = 0.028), interaction (NS). PC2: stress (NS), lineage (NS), interaction (NS). PC3: stress (NS), lineage (NS), interaction (F = 4.639, P = 0.040, qFDR = 0.055). PC4: stress (NS), lineage (F = 8.60, P = 0.007, qFDR = 0.021). Significance for both main effects and interactions were determined by using ANOVAs and a false discovery rate correction (with qFDR < 0.05 being significant).

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Fig. S3. Sample histograms and box plots for raw microarray signals (A and D) or for signals preprocessed with RMA GC content-adjusted algorithm (B, C, E, and D) for CRTX (A and C), BLA (A and B), CA1 (D and E), and CA3 (D and F).

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Fig. S4. Venn diagrams of four differentially expressed gene lists obtained by contrasting VNS V-L nonstress condition vs. C-L nonstress condition (NstV vs. NstC), V-L stress condition vs. C-L stress condition (StV vs. StC), C-L stress condition vs. C-L nonstress condition (StC vs. NstC), or V-L stress condition vs. V-L nonstress condition (StV vs. NstV) shown for CRTX (C), BLA (A), CA1 (B), and CA3 (D). (E, F, G, and H) Venn diagrams for the same lists showing how each of the four brain regions overlap. Numbers in brackets show number of differentially expressed probe sets.

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Fig. S5. Bar graph showing the number of genes differentially expressed and associated with functional categories in the brain. (A) BLA. (B) CRTX. (C) CA1. (D) CA3. Yellow, V-L nonstress vs. C-L nonstress differentially expressed genes (lists 1, 5, 9, and 13); green, V-L stress vs. C-L stress (lists 2, 6, 10, and 14); blue, C-L stress vs. C-L nonstress (lists 3, 7, 11, and 15); and red, V-L stress vs. V-L nonstress (lists 4, 8, 12, 16).

Fig. S6. Olfactory transduction pathway (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) showing genes affected by either CRS during adolescence (stress) or transgenerational epigenetic modification by vinclozolin (lineage) at least in one of four studied brain regions: CRTX, BLA, CA1, or CA3. Red box, up-regulated ; blue boxes, down-regulated; green boxes, not affected. Extended lists of genes for two pathway entities (R and PKA) are shown in beige boxes.

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Fig. S7. Calcium signaling pathway (A) and MAPK signaling pathway (B) (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) showing genes affected by either stress or lineage at least in one of four studied brain regions: CRTX, BLA, CA1, and CA3. Red boxes are up-regulated; blue boxes are down-regulated; and green boxes are not affected.

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Fig. S8. Subnetworks of shortest connections including cell processes for genes affected by either stress or lineage in BLA (combined gene lists 1–4; A) or CA3 (combined gene lists 13–16; B) obtained by global literature analysis using Pathway Studio 7.0 software (Ariadne Genomics). (A) For BLA, 49 affected genes of 125 genes (no ESTs included) are shown as red or blue. (B) For CA3, 60 affected genes of 198 genes (no ESTs) are shown as red or blue. The rest of affected genes are not connected and not shown. Oval and circle, protein; diamond, ligand; ice cream cone, receptor; circle/oval on tripod platform, transcription factor; crescent, protein kinase and kinase; irregular polygon, phosphatase. Red, up-regulated genes; blue, down-regulated genes; arrows with plus sign, positive regulation/activation; arrows with minus sign, negative regulation/inhibition; gray arrows, regulation; lilac, expression; purple, binding; green, promoter binding.

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Fig. S9. Images of different stages of brain processing. (A) Rats from one dyad were processed simultaneously. Before freezing, the brain was cut sagittally along the midline. The symmetrical brain halves were then recombined with one side from the vinclozolin individual and the other from the control individual; the sides used were alternated to control for possible asymmetries in activity. One such “brain” was used for metabolic studies and the other for RNA studies. (AA) Brain in sagittal block. (AB) Razor cutting brain along midline in sagittal plane. (AC) Two halves of brain shown. (AD) Recombining of brain halves; one half is from the V-L individual and the other from the C-L individual in the dyad. (AE) Brain being blocked into 2-mm slices. (AF) Target slices of recombined brain. (AG) Frozen slices of recombined brain showing 1-mm punches on one half (one individual) of sampled brain areas. (B) Cytochrome oxidase histochemistry of 40-μm sections of a recombined brain (left half is from V-L individual and right half is from C-L individual). Different levels indicate different brain regions analyzed: BLA, CA1, and CA3.

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Table S1. Metabolic activity (abundance of cytochrome oxidase) in brain nuclei in V-L and C-L male rats that received CRS during adolescence Mean activity value

Percentage of maximum

Percentage change

Nucleus

CNS

VNS

CS

VS

CNS

VNS

CS

VS

CNS vs. VNS

CS vs. VS

CNS vs. CS

VNS vs. VS

BLA BnSTl BnSTm CA1 CA3 CeAmy CoAmy CRTX MeAmy MePD MPOA PMCo ST VMH

207.70 208.82 205.58 157.95 159.54 175.72 159.91 223.69 152.50 205.56 201.14 221.05 245.28 202.36

198.80 204.36 197.59 157.41 156.31 178.02 152.69 236.90 162.73 203.31 197.50 182.06 247.57 191.03

213.36 203.06 204.33 152.34 160.11 174.78 161.40 235.57 166.48 226.58 198.19 210.09 241.44 207.71

200.69 207.47 201.59 141.65 142.16 168.64 157.46 229.76 165.13 185.28 189.12 180.53 274.92 202.27

97.3 100.0 100.0 100.0 99.6 98.7 99.1 94.4 91.6 90.7 100.0 100.0 89.2 97.4

93.2 97.9 96.1 99.7 97.6 100.0 94.6 100.0 97.7 89.7 98.2 82.4 90.0 92.0

100.0 97.2 99.4 96.4 100.0 98.2 100.0 99.4 100.0 100.0 98.5 95.0 87.8 100.0

94.1 99.4 98.1 89.7 88.8 94.7 97.6 97.0 99.2 81.8 94.0 81.7 100.0 97.4

−4.2 −2.1 −3.9 −0.3 −2.0 1.3 −4.5 5.6 6.1 −1.0 −1.8 −17.64 0.8 −5.5

−5.9 2.1 −1.3 −6.8 −11.2 −3.5 −2.4 −2.5 −0.8 −18.2 −4.5 −13.4 12.2 −2.6

2.7 −2.8 −0.6 −3.6 0.4 −0.5 0.9 5.0 8.4 9.3 −1.5 −5.0 −1.4 2.6

0.9 1.5 1.9 −10.0 −8.8 −5.3 3.0 −3.0 1.4 −8.0 −4.2 −0.7 10.0 5.4

Control Non-Stress PMCo

Vinclozolin Non-Stress

meAmy; MePD Lineage Effect

Control Stress

Stress Effect

CA1, CCAA3, MePD, ST

CA3; MePD; PMCo; ST Vinclozolin Stress

Boldface values in the percentage change columns indicate comparisons that were equal to or greater than 8% change. Schematic indicates those bolded nuclei in terms of comparison (lineage comparisons vertical vs. stress comparisons horizontal), indicated in the center cell of the 3 × 3 grid.

Table S2. Abbreviations for brain nuclei imaged for cytochrome histochemistry abundance (per ref. 1) Abbreviation BLA BnSTl BnSTm CA1 CA3 CeAmy CoAmy CRTX MeAmy MePD MPOA PMCo PVN ST VMH

Definition Basolateral amygdaloid nucleus Bed nucleus of the stria terminalis, anterolateral division Bed nucleus of the stria terminalis, anteromedial division CA1 area of the hippocampus CA3 area of the hippocampus Central amygdaloid nucleus Anterior cortical amygdaloid nucleus Primary and secondary motor cortex Medial amygdaloid nucleus Medial amygdaloid nucleus, posterior dorsal part Medial preoptic area Posteromedial cortical amygdaloid nucleus Periventricular hypothalamic nucleus Stria terminalis Ventromedial hypothalamic nucleus

1. Paxinos G, Watson C (2007) The Rat Brain in Stereotaxic Coordinates (Academic, New York).

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Table S3. List no. BLA 1 2 3 4 CRTX 5 6 7 8 CA1 9 10 11 12 CA3 13 14 15 16

Table S4.

Altered gene sets for V-L and C-L male rats subjected to CRS during adolescence Effect

Comparison

No. of altered genes

Lineage Lineage Stress Stress

Nonstress V-L vs. nonstress C-L Stress V-L vs. stress C-L Stress C-L vs. nonstress C-L Stress V-L vs. nonstress V-L

79 101 81 62

Lineage Lineage Stress Stress

Nonstress V-L vs. nonstress C-L Stress V-L vs. stress C-L Stress C-L vs. nonstress C-L Stress V-L vs. nonstress V-L

118 142 290 96

Lineage Lineage Stress Stress

Nonstress V-L vs. nonstress C-L Stress V-L vs. stress C-L Stress C-L vs. nonstress C-L Stress V-L vs. nonstress V-L

68 155 118 379

Lineage Lineage Stress Stress

Nonstress V-L vs. nonstress C-L Stress V-L vs. stress C-L Stress C-L vs. nonstress C-L Stress V-L vs. nonstress V-L

64 23 50 202

Number of altered genes in specific brain regions according to signaling pathways and cellular processes No. of genes altered in tissue list no.

Pathway name Olfactory transduction Calcium signaling pathway Neuroactive ligand–receptor interaction MAPK signaling pathway Huntington disease Pathways in cancer Endocytosis Alzheimer’s disease Cell adhesion molecules (CAMs) Cytokine–cytokine receptor interaction Axon guidance Metabolism of xenobiotics by P450 Drug metabolism, cytochrome P450 Phagosome Oxidative phosphorylation Parkinson disease Retinol metabolism Regulation of actin cytoskeleton PPAR signaling pathway

No. of altered genes 78 18 16 13 13 12 11 11 10 10 9 9 9 9 9 9 8 8 8

BLA

CRTX

CA1

CA3

1

2

3

4

5

6

7

8

9

10

11

12

3 1 1

4

1

4

6 1 2

17 3 2

2

3 1

9 1

3

1 1

2 1 1 1

8 4 3 1 1

2 1 1 2

1 4 1

17 6 7 4 3 3 4 3 3 5 2 4 4 4 1 2 2 2 4

1

1 1

1 1 2 1

1

1 3

2 1 1

1 1 1

1 2 2 1 2 3 4

1

1

3 5 1 1 1 4

1 1 1 2 2

1 1 1 1

1

1 1

1 2

1 1

1 1

4 1

2 2 4 4

13

1 1 1

14

15

16

4 1

2

9 1 2 1 2 2 1

1 1 1

3

1 1

2 2 1

Dataset S1. Genes expressed differentially in four brain regions in lineage and stress comparisons Dataset S1 (PDF)

Crews et al. www.pnas.org/cgi/content/short/1118514109

17 of 17

Supplemental Dataset S1. Genes Expressed Differentially in Four F3-Rat Brain Regions in Lineage and Stress Comparisons (16 gene lists)




1


List 1. Genes Expressed Differentially in Non-Stressed F3-Vinclozolin Rat Basolateral Amygdala as Compared to Non-Stressed F3-Control ('Nst-Vin vs Nst-Con' contrast), 79 genes and EST's GenBank_Reference Sequence

Mean _diff

Ratio

Affymetrix ID

Rg9mtd1 LOC365114 Growth Factors Bmp5 Mid1 Immune Response Spag6 Metabolism & Transport Doc2b Retsat Proteolysis

NM_001008337 ENSRNOT00000018945

-25 -36

0.83 0.82

10750795 10703187

RNA (guanine-9-) methyltransferase domain containing 1 similar to High mobility group protein 1 (HMG-1)

NM_001108168 NM_022927

15 -44

1.24 0.83

10911711 10937624

bone morphogenetic protein 5 midline 1

NM_001034960

62

1.23

10752563

sperm associated antigen 6

NM_031142 NM_145084

-25 94

0.83 1.26

10744970 10856424

double C2-like domains, beta retinol saturase (all trans retinol 13,14 reductase)

Serpina3k Receptors & Binding Proteins

NM_012657

-47

0.68

10891991

serine (or cysteine) peptidase inhibitor, clade A, member 3K

Klra5 Ly49s5 Olr1149 Olr1233 Olr1571 Htr5b Efcab1 Signaling Stac2

NM_198746 ENSRNOT00000045309 NM_001000874 NM_001001084 ENSRNOT00000034210 NM_024395 NM_001106930

16 23 17 -42 24 -15 42

1.27 1.22 1.29 0.76 1.27 0.81 1.29

10866236 10866180 10915281 10909168 10752574 10767186 10931558

killer cell lectin-like receptor, subfamily A, member 5 Ly49 stimulatory receptor 4 olfactory receptor 1149 olfactory receptor 1233 olfactory receptor 1571 5-hydroxytryptamine (serotonin) receptor 5B EF hand calcium binding domain 1

NM_001108834

38

1.28

10746842

Mrgprb5 Sh2d1b1 Tpte Transcription Npas4 Set Translation & Protein Modification RGD1564552 Miscellaneous & Unknown

NM_001002284 ENSRNOT00000048692 NM_001108877

47 -10 10

1.21 0.79 1.22

10707154 10765469 10792456

SH3 and cysteine rich domain 2 MAS-related G protein-coupled receptor, member B5 SH2 domain protein 1B1 transmembrane phosphatase with tensin homology

NM_153626 NM_001012504

31 -164

1.20 0.80

10727717 10749869

neuronal PAS domain protein 4 SET nuclear oncogene

ENSRNOT00000050803

-141

0.73

10799888

similar to ribosomal protein L21

LOC288521 RGD1311849 RGD1565119 Ccdc162 rno-mir-21

BC079301 ENSRNOT00000058387 ENSRNOT00000048106 ENSRNOT00000000340 rno-mir-21 XM_002725832

-12 26 -14 13 30 -9

0.76 1.22 0.79 1.25 1.25 0.80

10760760 10869837 10776873 10833727 10745931 10831802

Gene Symbol

Gene Title

Epigenetics




2


similar to Leukosialin precursor (Leucocyte sialoglycoprotein) (Sialophorin) (CD43) (W3 similar to mKIAA1797 protein similar to Mitochondrial carrier triple repeat 1 coiled-coil domain containing 162 rCG44733-like

LOC100363863 EST's LOC363737

ENSRNOT00000032643 XR_008519 XR_008445 XR_007871 XR_007680 XR_007365 XR_006323 XR_005743 XR_005657 XR_005430 XM_226468 NC_001665 ENSRNOT00000060361 ENSRNOT00000053328 ENSRNOT00000053029 ENSRNOT00000052710 59896131, 41350416 -------------------------------------------------------------------

-9 -24 -121 -198 15 -115 -10 -7 -20 63 36 -1186 29 -232 32 -101 12 -1953 -127 -88 -80 -58 -49 -42 -15 -13 -7 4 6 7 8 8 8 9 10 12 12 12 12 13 14 18 19 19 20 21 21 27 28 29

0.78 0.82 0.78 0.83 1.27 0.83 0.82 0.82 0.79 1.24 1.30 0.74 1.25 0.76 1.25 0.79 1.30 0.74 0.81 0.83 0.80 0.82 0.77 0.79 0.76 0.82 0.79 1.23 1.23 1.21 1.20 1.22 1.24 1.28 1.24 1.27 1.23 1.27 1.22 1.26 1.21 1.24 1.22 1.20 1.22 1.23 1.29 1.23 1.30 1.24

10750089 10732906 10880562 10927699 10791977 10813246 10923292 10937252 10898947 10877896 10807925 10930595 10889368 10855946 10774265 10838282 10769693 10930580 10772758 10811008 10761245 10711498 10864479 10832081 10795677 10836152 10870488 10814661 10932910 10936478 10709532 10799500 10768128 10716744 10702076 10884614 10815913 10820963 10781972 10785259 10782889 10893434 10861656 10917344 10816647 10726652 10776796 10813005 10815350 10873885

hypothetical LOC363737

List 2. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat Basolateral Amygdala as Compared to Stressed F3-Control ('St-Vin vs St-Con' contrast), 101 genes and EST's Gene Symbol




GenBank_Reference

Mean

Ratio

Affymetrix

3


Gene Title

Sequence Cell Cycle Cdca3 CytoskeletonECM Pcdhb6 Development

_diff

ID

NM_001007648

-46

0.80

10858707

cell division cycle associated 3

NM_001014780

47

1.24

10801176

protocadherin beta 6

Opalin Mtpn Growth Factors Bdnf Metabolism & Transport Kcnt2 LOC685173 Proteolysis

NM_001017386 AY951952

-66 -11

0.79 0.83

10730148 10861826

oligodendrocytic myelin paranodal and inner loop protein myotrophin

NM_012513

25

1.21

10852620

brain derived neurotrophic factor

NM_198762 XM_001062675

79 -18

1.26 0.77

10764460 10899693

potassium channel, subfamily T, member 2 similar to carbonic anhydrase 13

RGD1560658 Receptors & Binding Proteins Olr1171 Olr1742 Olr349 Olr679 Olr720 Signaling

ENSRNOT00000022681

10

1.31

10798126

serine (or cysteine) peptidase inhibitor, clade B, member 1b

NM_001001005 NM_001001424 NM_001001019 NM_001000354 NM_001001067

17 13 23 16 28

1.28 1.26 1.32 1.23 1.21

10915295 10827655 10729045 10847168 10847229

olfactory receptor 1171 olfactory receptor 1742 olfactory receptor 349 olfactory receptor 679 olfactory receptor 720

Arap2 Ctxn2 RGD1562952 Transcription

ENSRNOT00000044580 NM_001162935 ENSRNOT00000061017

-18 36 -238

0.78 1.25 0.72

10772895 10839365 10812779

ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2 cortexin 2 similar to Erbb2 interacting protein isoform 2 similar to High mobility group protein 1 (HMG-1) (High mobility group protein B1) (Amphoterin) (Heparin-binding protein p30) SET nuclear oncogene

LOC365114 Set Translation & Protein Modification Rps27a RGD1562547

ENSRNOT00000018945 NM_001012504

-37 -189

0.83 0.80

10703187 10749869

ENSRNOT00000042383 ENSRNOT00000049211

-110 -62

0.81 0.82

10734318 10901960

RGD1564400 RGD1564552 Miscellaneous & Unknown LOC686096 EST's MGC72627 RGD1560493

ENSRNOT00000033258 ENSRNOT00000050803

-87 -112

0.81 0.78

10836556 10799888

similar to thymosin, beta 4 similar to ribosomal protein L31 similar to Eukaryotic translation initiation factor 5 (eIF-5) similar to ribosomal protein L21

XM_002730304

-116

0.82

10939909

similar to basic transcription factor 3

BC061963 ENSRNOT00000032053 XR_008237 XR_007324 XR_007098 XR_009222 XR_008445

55 21 -38 -23 -20 -50 -162

1.20 1.24 0.80 0.80 0.83 0.69 0.72

10853407 10937331 10926160 10877933 10707370 10729312 10880562

similar to RIKEN cDNA A330021E22 similar to chromosome X open reading frame 45




4


XR_007232 XR_005958 XR_008485 XR_008126 XR_007395 XR_009494 NC_001665




6683748 ENSRNOT00000059477 ENSRNOT00000057420 ENSRNOT00000056786 ENSRNOT00000054649 ENSRNOT00000054517 ENSRNOT00000053934 ENSRNOT00000052710 ENSRNOT00000052697 ENSRNOT00000052541 ENSRNOT00000018011

-14 -9 -12 9 -13 -8 -1372 -70 -105 -105 -145 -189 -107 -363 -130 12 -30 -15

0.75 0.82 0.83 1.29 0.70 0.82 0.60 0.79 0.69 0.69 0.67 0.82 0.67 0.82 0.76 1.27 0.69 0.76

10784444 10793706 10794940 10822090 10850440 10739816 10930588 10748234 10791602 10833416 10939699 10930226 10797013 10722465 10838282 10878963 10911811 10926819

ENSRNOT00000039948 -------------------------------------------------------------------------

-36 -263 -583 -83 -65 -58 -58 -54 -35 -28 -21 -20 -17 -16 -13 -12 -11 -5 6 7 8 8 9 9 9 10 11 11 11 12 12 12 13 13 13 13 13

0.82 0.74 0.80 0.81 0.83 0.81 0.81 0.77 0.79 0.80 0.78 0.71 0.78 0.79 0.78 0.81 0.83 0.81 1.20 1.22 1.22 1.30 1.23 1.20 1.24 1.26 1.27 1.25 1.22 1.21 1.28 1.22 1.26 1.25 1.32 1.23 1.23

10767044 10722451 10722481 10869614 10846749 10756253 10756255 10858497 10853681 10764400 10907958 10925371 10769398 10773706 10746252 10776665 10795677 10757702 10853227 10724580 10751226 10718406 10823430 10782954 10931079 10812884 10870012 10785259 10778575 10717396 10922247 10795717 10857000 10781972 10893404 10887074 10752096

5


-----------------------------

14 15 17 17 17 18 25 25 25 27 29 30 39 40

1.20 1.26 1.20 1.26 1.29 1.23 1.43 1.41 1.24 1.23 1.23 1.30 1.31 1.29

10711257 10707254 10792099 10890570 10917318 10868794 10939931 10920630 10939899 10801707 10909070 10772554 10846650 10791561

List 3. Genes Expressed Differentially in Stressed F3-Control Rat Basolateral Amygdala as Compared to NonStressed F3-Control ('Str-Con vs Nst-Con' contrast), 81 genes and EST's Mean _diff

Ratio

Affymetrix ID

NM_001109227 NM_130411 NM_031352

-85 -152 -56

0.81 0.76 0.83

10854199 10725806 10773999

tetraspanin 33 coronin, actin binding protein 1A drebrin-like

NM_144762 NM_001109003 NM_031070 NM_001107825

-53 -141 -274 -26

0.82 0.62 0.83 0.83

10896250 10912718 10906546 10844082

RGD1563738 Sprn Synj2 Synpo2 Tmem59l

ENSRNOT00000052026 NM_001031845 NM_001113371 ENSRNOT00000019931 BC089056

20 -83 -106 8 -110

1.29 0.79 0.67 1.20 0.81

10909263 10726620 10702829 10826541 10787556

Trpc4 Epigenetics Cog7 Growth Factors Bdnf Fgf1 Immune Response Igha

NM_080396

-83

0.62

10815352

brain and acute leukemia, cytoplasmic copine IV NEL-like 2 (chicken) netrin G2 similar to Discs, large homolog 5 (Placenta and prostate DLG) shadow of prion protein homolog (zebrafish) synaptojanin 2 synaptopodin 2 transmembrane protein 59-like transient receptor potential cation channel, subfamily C, member 4

NM_001033889

-41

0.82

10725427

component of oligomeric golgi complex 7

NM_012513 NM_012846

-25 9

0.83 1.26

10852620 10804127

brain derived neurotrophic factor fibroblast growth factor 1

BC092592

18

1.29

10892572

Klra7 Mal2 Metabolism & Transport

XM_578407 NM_198786

23 -356

1.45 0.72

10866140 10896533

immunoglobulin heavy chain, alpha killer cell lectin-like receptor, subfamily A, member 7 mal, T-cell differentiation protein 2

Kcnj9 Kcnn2 Kcnt2 Atp6v1a

NM_053834 NM_019314 NM_198762 NM_001108318

-20 -67 -125 -536

0.81 0.82 0.71 0.81

10770022 10801520 10764460 10823609

potassium inwardly-rectifying channel, subfamily J, member 9 potassium intermediate potassium channel, subfamily T, member 2 ATPase, H+ transporting, lysosomal V1 subunit A

Gene Symbol CytoskeletonECM Tspan33 Coro1a Dbnl Development Baalc Cpne4 Nell2 Ntng2




GenBank_Reference Sequence

6


Gene Title

Cth Fetub Msra Ppap2a Syp Faah LOC685173 Proteolysis Prcp Receptors & Binding Proteins Olr98 RGD1560871 Nrp1 Signaling

NM_017074 NM_053348 NM_053307 NM_022538 NM_012664 NM_024132 XM_001062675

-25 -26 -42 -114 -568 -82 16

0.83 0.78 0.78 0.78 0.82 0.77 1.25

10827517 10755148 10784517 10813048 10937103 10871182 10899693

cystathionase (cystathionine gamma-lyase) fetuin B methionine sulfoxide reductase A phosphatidic acid phosphatase type 2A synaptophysin fatty acid amide hydrolase similar to carbonic anhydrase 13

NM_001106281

-45

0.82

10708672

prolylcarboxypeptidase (angiotensinase C)

NM_001000143 ENSRNOT00000022951 NM_145098

16 -71 -45

1.22 0.79 0.70

10709432 10863960 10808959

olfactory receptor 98 similar to plexin 1 neuropilin 1

Cmtm4 Ehd3 Hpcal4 Ifi27l1

NM_001172151 NM_138890 NM_017357 NM_203410

-83 -108 -255 -168

0.83 0.79 0.81 0.79

10805716 10888596 10871732 10886573

Prkar1b RGD1561667

NM_001033679 ENSRNOT00000059957

-204 25

0.80 1.24

10757119 10703287

Shd Tmem74 Srgap1 Translation & Protein Modification Bin1 Ccdc32 Dnajb1 Translation RGD1562547 Rps21 Miscellaneous & Unknown Fam40a LOC501427 Wdr1 EST's LOC498145

NM_001108223 ENSRNOT00000006791 ENSRNOT00000006180

-29 -47 35

0.82 0.77 1.36

10931523 10903560 10902765

CKLF-like MARVEL transmembrane domain containing 4 EH-domain containing 3 hippocalcin-like 4 interferon, alpha-inducible protein 27 protein kinase, cAMP dependent regulatory, type I, beta similar to putative protein kinase src homology 2 domain-containing transforming protein D transmembrane protein 74 SLIT-ROBO Rho GTPase activating protein 1

NM_053959 NM_001024245 NM_001108441

-210 -111 -74

0.83 0.80 0.77

10800760 10848499 10810295

bridging integrator 1 coiled-coil domain containing 32 DnaJ (Hsp40) homolog, subfamily B, member 1

ENSRNOT00000049211 NM_031111

67 104

1.24 1.23

10901960 10873649

similar to ribosomal protein L31 ribosomal protein S21

ENSRNOT00000025036 ENSRNOT00000061060 NM_001014135

-46 9 -165

0.80 1.26 0.83

10825830 10779531 10773205

family with sequence similarity 40, member A similar to Spetex-2F protein WD repeat domain 1

NM_001017485 ENSRNOT00000048364 ENSRNOT00000052541 ENSRNOT00000057420 ENSRNOT00000059477 NC_001665 NC_001665 ---------------

-57 -14 27 112 112 1587 1419 -51 -18 -15 -11 -9 -8 -5

0.81 0.76 1.39 1.49 1.49 1.35 1.69 0.70 0.77 0.82 0.75 0.81 0.83 0.83

10760393 10900112 10911811 10833416 10791602 10930595 10930588 10755315 10917318 10782179 10707639 10850610 10931079 10891491

similar to RIKEN cDNA 2810453I06




7


----XR_007232 ------XR_008088 -------------------

8 9 10 10 10 11 12 12 34 36 45 51 66 66 807 969

1.30 1.30 1.23 1.27 1.24 1.22 1.24 1.23 1.25 1.21 1.36 1.28 1.28 1.28 1.26 1.29

10856117 10850313 10784444 10909127 10702076 10776665 10786415 10818253 10853681 10847062 10914009 10858497 10756253 10756255 10930622 10930560

List 4. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat Basolateral Amygdala as Compared to Non-Stressed F3-Vinclozolin ('Str-Vin vs Nst-Vin' contrast), 62 genes and EST's Gene Symbol

GenBank_Reference Sequence

Mean _diff

Ratio

Affymetrix ID

Gene Title

Development Gdap1l1

NM_001107798

-47

0.83

10842001

LOC689690 Nptx2

ENSRNOT00000052385 NM_001034199

39 -106

1.44 0.74

10809503 10760290

RGD1563738 Sntb2 Electron Transport

ENSRNOT00000052026 NM_001168674

15 37

1.21 1.21

10916360 10807601

ganglioside-induced differentiation-associated protein 1-like 1 similar to Discs large homolog 5 (Placenta and prostate DLG) (Discs large protein P-dlg) neuronal pentraxin 2 similar to Discs, large homolog 5 (Placenta and prostate DLG) syntrophin, beta 2

Cyp26b1 Epigenetics LOC689244 LOC501799 Immune Response Igsf21 RT1-CE10 Metabolism & Transport

NM_181087

-31

0.77

10863608

cytochrome P450, family 26, subfamily b, polypeptide 1

ENSRNOT00000061517 ENSRNOT00000061397

127 163

1.50 1.34

10756280 10756257

similar to chromobox homolog 3 similar to chromobox homolog 3

ENSRNOT00000051793 NM_001008833

-52 29

0.81 1.26

10880936 10828001

immunoglobin superfamily, member 21 RT1 class I, locus CE10

Kcna6

NM_023954

-75

0.81

10865738

Kcnj9 Alas2 Decr1 Hpgd Proteolysis

NM_053834 NM_013197 NM_057197 NM_024390

-20 17 51 17

0.82 1.21 1.23 1.29

10770022 10932912 10875631 10791522

potassium voltage gated channel, shaker related subfamily, member 6 potassium inwardly-rectifying channel, subfamily J, member 9 aminolevulinate, delta-, synthase 2 2,4-dienoyl CoA reductase 1, mitochondrial hydroxyprostaglandin dehydrogenase 15 (NAD)

RGD1559940 Receptors & Binding

ENSRNOT00000038310

12

1.20

10900050

similar to ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans)




8


Proteins Olr1093 Olr1117 Olr668 Olr995 Grm2 LOC304239 Vom2r1 Vom2r2 Signaling Arrb2 Exph5 RGD1560209 Sh2d1b1 Stac2 Transcription Junb Mtpn Znf622 Miscellaneous & Unknown LOC501427 RGD1561734 EST's LOC363337

NM_001001388 NM_001000884 NM_001000348 NM_001000938 NM_001105711 ENSRNOT00000049215 NM_001099460 ENSRNOT00000051591

41 -15 -12 16 -65 37 27 8

1.23 0.81 0.80 1.30 0.67 1.27 1.24 1.20

10901100 10915199 10847146 10893373 10919953 10756334 10701668 10701636

olfactory receptor 1093 olfactory receptor 1117 olfactory receptor 668 olfactory receptor 995 glutamate receptor, metabotropic 2 similar to RalA binding protein 1 vomeronasal 2 receptor, 3 vomeronasal 2 receptor, 2

NM_012911 ENSRNOT00000039336 ENSRNOT00000047232 ENSRNOT00000048692 NM_001108834

-43 -19 15 9 -36

0.82 0.81 1.20 1.24 0.79

10735205 10909987 10796831 10765469 10746842

arrestin, beta 2 exophilin 5 similar to MAP SH2 domain protein 1B1 SH3 and cysteine rich domain 2

NM_021836 AY951952 NM_001034912

-25 -11 -94

0.80 0.82 0.83

10806585 10861826 10813934

jun B proto-oncogene myotrophin family with sequence similarity 134, member B

ENSRNOT00000061060 ENSRNOT00000056348

8 -53

1.28 0.79

10779531 10925933

similar to Spetex-2F protein similar to KIAA1913

BC082068 XR_007680 XR_006025 XM_001080565 NC_001665 NC_001665 ENSRNOT00000055830 ENSRNOT00000053106 ENSRNOT00000053029 ENSRNOT00000040251 59896131, 41350416 -----------------------------------

31 -14 -5 51 1455 804 66 -12 -30 -9 -14 -31 -54 -23 -11 -9 -7 5 5 11 19 25 37 48 151 763 930 2253

1.21 0.79 0.80 1.21 1.43 1.62 1.23 0.83 0.82 0.83 0.72 0.75 0.83 0.76 0.83 0.81 0.81 1.22 1.24 1.29 1.21 1.28 1.22 1.42 1.21 1.27 1.36 1.41

10931083 10791977 10775566 10729852 10930595 10930588 10859162 10908229 10774265 10868279 10769693 10815350 10871661 10775577 10932132 10929592 10729120 10746914 10852168 10857203 10809071 10802574 10864479 10726672 10718134 10930560 10930622 10930580

similar to RIKEN cDNA 1700081O22

List 5. Genes Expressed Differentially in Non-Stressed F3-Vinclozolin Rat Cortex Region as Compared to NonStressed F3-Control ('Nst-Vin vs Nst-Con' contrast), 118 genes and EST's Gene Symbol




GenBank_Reference

Mean

Ratio

Affymetrix

9


Gene Title

Sequence

_diff

ENSRNOT00000060484

28

1.22

10801204

protocadherin beta 19

NM_001004083

57

1.22

10719958

LOC681385 Electron Transport

ENSRNOT00000067576

6

1.23

10843857

EGL nine homolog 2 (C. elegans) similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4)

Cyp2r1 LOC305698 Epigenetics Mettl11a Hist1h4b Growth Factors Ccl27 Hormones Gphb5 Pth Immune Response Btnl7 Ly6b Slamf9 Metabolism & Transport Akr1b7

NM_001108499 ENSRNOT00000049636

-13 -28

0.79 0.83

10725045 10779240

cytochrome P450, family 2, subfamily r, polypeptide 1 similar to RIKEN cDNA 1700001F09

NM_001025019 NM_022686

33 125

1.20 1.20

10835252 10798490

methyltransferase like 11A histone cluster 1, H4b

NM_001108660

90

1.22

10876193

chemokine (C-C motif) ligand 27

NM_001007013 NM_017044

-12 12

0.83 1.21

10890626 10724987

glycoprotein hormone beta 5 parathyroid hormone

NM_212488 NM_139257 NM_001105971

-40 6 -12

0.82 1.25 0.83

10828335 10904590 10765746

butyrophilin-like 7 lymphocyte antigen 6 complex, locus B SLAM family member 9

6

1.22

10854427

Akr1d1 Apool Bphl Commd8

NM_138884 NM_001014105 NM_001037206 NM_001106004

-15 -23 13 -28

0.78 0.81 1.25 0.83

10854548 10934700 10798100 10772517

Ndufa1 Nqo2

NM_001108813 NM_001004214

66 -58

1.20 0.69

10931991 10798119

Pafah1b3 Sepw1 Mgst1 Cerkl Proteolysis Slpil2 Receptors & Binding Proteins Agtr1b Epha8 Igfbp6 Olr1060 Olr1237 Olr1560 Olr29 Olr481

NM_053654 NM_013027 NM_134349 ENSRNOT00000043238

-48 68 23 6

0.82 1.21 1.21 1.20

10719817 10719212 10859392 10846671

aldo-keto reductase family 1, member B7 aldo-keto reductase family 1, member D1 (delta 4-3ketosteroid-5-beta-reductase) apolipoprotein O-like biphenyl hydrolase-like (serine hydrolase) COMM domain containing 8 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1 NAD(P)H dehydrogenase, quinone 2 platelet-activating factor acetylhydrolase, isoform 1b, subunit 3 selenoprotein W, 1 microsomal glutathione S-transferase 1 ceramide kinase-like

NM_001008872

13

1.29

10851573

antileukoproteinase-like 2

-17 -15 -149 26 11 27 24 -13

0.82 0.81 0.62 1.68 1.28 1.22 1.35 0.83

10822516 10880738 10899465 10900087 10909176 10750649 10723519 10846950

angiotensin II receptor, type 1b Eph receptor A8 insulin-like growth factor binding protein 6 olfactory receptor 1060 olfactory receptor 1237 olfactory receptor 1560 olfactory receptor 29 olfactory receptor 481

CytoskeletonECM Pcdhb19 Development Egln2




NM_053781

NM_031009 ENSRNOT00000017559 NM_013104 NM_001000698 NM_001000963 NM_001001009 NM_001000691 NM_001000684

ID

10


Olr631 Olr703 Olr724 Taar8a Signaling LOC689617 Mrgprb4 Rassf9 Scube1 Snx11 Transcription

NM_001000339 NM_001000359 NM_001000573 NM_175599

-49 7 -12 8

0.81 1.20 0.80 1.23

10847113 10847193 10847233 10717268

olfactory receptor 631 olfactory receptor 703 olfactory receptor 724 trace amine-associated receptor 8a

ENSRNOT00000058250 ENSRNOT00000045792 NM_022959 NM_001134884 NM_001012012

36 -43 -12 38 51

1.36 0.73 0.83 1.21 1.23

10815215 10722218 10895247 10905843 10746594

similar to GTPase activating protein testicular GAP1 MAS-related GPR, member B4 Ras association (RalGDS signal peptide, CUB domain, EGF-like 1 sorting nexin 11

Chchd2

NM_001015019

113

1.31

10930091

Chchd6 Fbxo23 Nola2 Ry1 Top1mt Translation & Protein Modification RGD1564552 Rpl22l1 Rpl36 Miscellaneous & Unknown LOC501427 Lrrn4 Magohb RGD1310587 RGD1565493 Samd12 Ttc36 RGD1565166 RGD1566243

NM_001106608 NM_001013138 NM_001105779 NM_001108636 NM_001002798

90 122 90 -53 16

1.23 1.27 1.21 0.81 1.21

10863993 10797368 10733380 10782583 10904612

coiled-coil-helix-coiled-coil-helix domain containing 2 coiled-coil-helix-coiled-coil-helix domain containing 6 F-box only protein 23 NHP2 ribonucleoprotein homolog (yeast) small nuclear ribonucleoprotein 27kDa (U4 topoisomerase (DNA) I, mitochondrial

ENSRNOT00000050803 NM_001108548 NM_022504

-97 -73 91

0.69 0.82 1.36

10799888 10814650 10772984

similar to ribosomal protein L21 ribosomal protein L22 like 1 ribosomal protein L36

ENSRNOT00000061060 ENSRNOT00000040802 ENSRNOT00000013725 NM_001100857 XM_002729803 NM_001130562 NM_001005546 NM_001105762 NM_001134635

-14 -30 -18 -17 -11 -79 -34 10 -6

0.72 0.82 0.81 0.83 0.83 0.82 0.80 1.22 0.82

10779531 10850170 10866265 10770517 10903280 10903721 10916876 10731622 10909777

Utp3 EST's RGD1309501 LOC306766 RGD1310794

NM_001012036

22

1.20

10776064

similar to Spetex-2F protein leucine rich repeat neuronal 4 mago-nashi homolog B (Drosophila) similar to hypothetical protein FLJ14146 similar to DKFZP434I092 protein sterile alpha motif domain containing 12 tetratricopeptide repeat domain 36 similar to MGC45438 protein similar to protein of unknown function UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae)

-30 114 -23 -35 12 -17 -50 29 30 70 -31 -108 311 28 -278 -85 -60

0.79 1.31 0.81 0.75 1.30 0.81 0.79 1.46 1.35 1.21 0.83 0.60 1.35 1.24 0.69 0.73 0.83

10774403 10794172 10853515 10845365 10731555 10828152 10717829 10934560 10930610 10918820 10884046 10939699 10708691 10938712 10760298 10827665 10798921




NM_001127537 NM_001014007 BC093393 XR_008339 XR_009246 XR_009095 XR_008340 XR_007585 NC_001665 K02909 ENSRNOT00000060122 ENSRNOT00000056786 ENSRNOT00000053279 ENSRNOT00000042423 37727288 -----

11


hypothetical LOC305552 hypothetical LOC306766 similar to RIKEN cDNA C030048B08

---------------------------------------------------------------------------------

-45 -41 -39 -35 -35 -34 -34 -31 -30 -28 -27 -21 -21 -14 -12 -10 -10 -10 -10 -9 -9 -8 -7 -5 8 8 9 11 13 13 14 14 16 21 26 27 34 44 56 184

0.79 0.77 0.80 0.82 0.83 0.66 0.82 0.69 0.82 0.80 0.81 0.82 0.80 0.83 0.75 0.82 0.83 0.83 0.83 0.81 0.74 0.82 0.79 0.80 1.22 1.33 1.26 1.24 1.20 1.21 1.36 1.28 1.38 1.33 1.25 1.21 1.22 1.40 1.26 1.25

10932187 10767747 10726221 10914901 10803509 10866205 10760005 10717085 10888682 10927840 10795400 10820761 10750470 10848414 10873723 10802574 10813889 10823935 10877538 10706465 10841294 10769229 10740841 10746914 10711995 10891491 10744141 10772782 10778675 10822356 10896378 10814299 10877749 10917344 10909137 10884820 10826602 10856228 10714842 10805225

List 6. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat Cortex Region as Compared to Stressed F3Control ('St-Vin vs St-Con' contrast), 142 genes and EST's Gene Symbol Development Robld3 RGD1559751 Syt2 Vof16 Electron Transport Gpx8 Epigenetics LOC501799 Hist1h2bc




GenBank_Reference Sequence

Mean _diff

Ratio

Affymetrix ID

Gene Title

NM_001106441 ENSRNOT00000058177 NM_012665 NM_147207

-30 -14 -84 91

0.78 0.80 0.83 1.58

10824344 10805591 10764174 10909382

roadblock domain containing 3 similar to n-chimaerin synaptotagmin II ischemia related factor vof-16

NM_001106411

29

1.23

10821367

glutathione peroxidase 8

ENSRNOT00000061397 NM_001109400

100 44

1.38 1.34

10759844 10798475

similar to chromobox homolog 3 histone cluster 1, H2bc

12


Mkx Growth Factors Ctgf Hdgfl1 Immune Response RT1-S2 Igha Metabolism & Transport Akr1c19 Cml1 Fth1 Gnpnat1

ENSRNOT00000025623

-24

0.82

10798902

mohawk homeobox

NM_022266 NM_133549

47 12

1.31 1.24

10717233 10795072

connective tissue growth factor hepatoma derived growth factor-like 1

NM_001008857 BC092592

15 20

1.35 1.34

10827789 10892572

RT1 class Ib, locus S2 immunoglobulin heavy chain, alpha

NM_001100576 NM_021668 BC081845 NM_001134756

8 -34 43 71

1.20 0.82 1.26 1.22

10796050 10863692 10713831 10782846

Hsd3b6 Klk8

NM_017265 NM_001107509

-27 -27

0.82 0.80

10825349 10706424

Lrp1b

NM_001107843

54

1.23

10844966

Piga Pln

NM_001108816 NM_022707

53 18

1.25 1.24

10937719 10830174

LOC679586 RGD1565045 RGD1561777 Proteolysis Ube2n Receptors & Binding Proteins Fabp7 Hcrtr2 Igfbp6 Lhcgr Olr1199 Olr1223 Olr14 Olr1627 Olr1701 Olr421 Olr550 Olr850 LOC690821 LOC304239 P2rx5 Signaling Cyr61 Ibsp Pef1

ENSRNOT00000048808 ENSRNOT00000015997 ENSRNOT00000035047

-31 -11 -31

0.81 0.81 0.76

10920350 10716502 10833617

aldo-keto reductase family 1, member C19 camello-like 1 ferritin, heavy polypeptide 1 glucosamine-phosphate N-acetyltransferase 1 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 6 kallikrein related-peptidase 8 low density lipoprotein-related protein 1B (deleted in tumors) phosphatidylinositol glycan anchor biosynthesis, class A phospholamban similar to ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G similar to carboxylesterase isoenzyme gene similar to Na+ dependent glucose transporter 1

BC090072

26

1.42

10759435

ubiquitin-conjugating enzyme E2N

NM_030832 NM_013074 NM_013104 NM_012978 NM_001000819 NM_001000441 NM_001000695 NM_001000091 NM_001001114 NM_001000824 NM_001000322 NM_001000401 ENSRNOT00000047245 ENSRNOT00000049215 NM_080780

115 22 -82 -8 -19 32 11 -10 41 -14 -41 -5 -9 25 -19

1.27 1.20 0.67 0.81 0.77 1.47 1.26 0.83 1.21 0.80 0.82 0.82 0.82 1.39 0.83

10830223 10918761 10899465 10888343 10909109 10909149 10723503 10779790 10830802 10844764 10847051 10876763 10908225 10834046 10735647

fatty acid binding protein 7, brain hypocretin (orexin) receptor 2 insulin-like growth factor binding protein 6 luteinizing hormone olfactory receptor 1199 olfactory receptor 1223 olfactory receptor 14 olfactory receptor 1627 olfactory receptor 1701 olfactory receptor 421 olfactory receptor 550 olfactory receptor 850 similar to olfactory receptor Olr1185 similar to RalA binding protein 1 purinergic receptor P2X, ligand-gated ion channel, 5

NM_031327 NM_012587 NM_001007651

11 -16 -28

1.20 0.81 0.76

10827231 10775365 10901111

Plekho2 Prkacb Pygm Stk10 Trib2

ENSRNOT00000042633 NM_001077645 NM_012638 NM_019206 NM_001108015

-47 -40 -73 48 -35

0.78 0.77 0.83 1.25 0.83

10918288 10827305 10713382 10741887 10889263

cysteine-rich, angiogenic inducer, 61 integrin-binding sialoprotein penta-EF hand domain containing 1 pleckstrin homology domain containing, family O member 2 protein kinase, cAMP dependent, catalytic, beta phosphorylase, glycogen, muscle serine tribbles homolog 2 (Drosophila)




13


Transcription Casc5 Ccdc112 Ccdc153 Dpf3 Hlf Npas4 Nr4a2 Polr2j

ENSRNOT00000067081 NM_001109124 NM_001013953 ENSRNOT00000010703 ENSRNOT00000055664 NM_153626 NM_019328 NM_001105921

-16 29 -14 -23 -41 192 41 -36

0.79 1.23 0.78 0.83 0.81 1.53 1.23 0.82

10838743 10804371 10909463 10891013 10746209 10727717 10845384 10761070

Rprm Txnip Zcchc12 Zfp280b Zfp354a Zfpm2 Translation & Protein Modification RGD1561635 RGD1564552 Miscellaneous & Unknown FAM50A LOC680227

NM_001044276 NM_001008767 NM_001014065 NM_001106384 NM_052798 NM_001130501

78 170 40 -12 -11 32

1.52 1.48 1.27 0.83 0.83 1.24

10845372 10817552 10936360 10832460 10733310 10896337

cancer susceptibility candidate 5 coiled-coil domain containing 112 coiled-coil domain containing 153 D4, zinc and double PHD fingers, family 3 hepatic leukemia factor neuronal PAS domain protein 4 nuclear receptor subfamily 4, group A, member 2 polymerase (RNA) II (DNA directed) polypeptide J reprimo, TP53 dependent G2 arrest mediator candidate thioredoxin interacting protein zinc finger, CCHC domain containing 12 zinc finger protein 280b zinc finger protein 354A zinc finger protein, multitype 2

ENSRNOT00000032135 ENSRNOT00000050803

-10 -45

0.81 0.80

10764811 10799888

similar to 40S ribosomal protein S17 similar to ribosomal protein L21

NM_001170573 NM_001047974

27 -7

1.24 0.82

10940358 10934517

family with sequence similarity 50, member A LRRGT00193

LOC100363176 Spetex-2A Trim59 RGD1562420 rno-mir-9-1 EST's LOC500492

XM_002725742 ENSRNOT00000061476 NM_001108945 ENSRNOT00000007683 rno-mir-9-1

-43 14 29 -31 36

0.75 1.29 1.21 0.69 1.24

10728981 10782777 10823591 10887809 10816485

mCG145114-like Spetex-2B protein tripartite motif-containing 59 similar to hypothetical protein

XR_005747 NM_001111127 J01884 ENSRNOT00000057306 ENSRNOT00000054517 ENSRNOT00000053338 ENSRNOT00000053279 ENSRNOT00000053268 ENSRNOT00000053042 ENSRNOT00000052741 ENSRNOT00000052710 ENSRNOT00000025383 AF272707 AF188753 XR_005716 XM_221100 XR_006516 XR_006465 XR_005810 XR_007276 XR_007404 XM_001066244 -----

30 66 -51 -274 -39 -25 -252 287 69 24 -74 103 -22 -183 -11 60 -45 -13 -37 -23 -113 -44 -621 -411

1.22 1.38 0.77 0.78 0.76 0.83 0.79 1.42 1.53 1.30 0.72 1.24 0.80 0.78 0.83 1.26 0.82 0.72 0.83 0.83 0.80 0.82 0.81 0.75

10877982 10798473 10830454 10815996 10797013 10791520 10708691 10909356 10937568 10726878 10838282 10920986 10867318 10855185 10875005 10748601 10759585 10902361 10849861 10933574 10845645 10905605 10761253 10758031




14


-----------------------------------------------------------------------------------------------

-91 -58 -52 -47 -44 -43 -42 -37 -35 -35 -26 -22 -20 -18 -16 -13 -13 -10 -10 -10 -8 -7 -6 8 9 10 18 18 18 19 20 26 26 26 26 26 29 32 36 36 50 50 64 73 172 237 257

0.79 0.81 0.74 0.81 0.71 0.73 0.78 0.76 0.80 0.78 0.75 0.76 0.77 0.82 0.82 0.82 0.79 0.82 0.83 0.79 0.83 0.75 0.82 1.34 1.22 1.24 1.26 1.36 1.25 1.40 1.24 1.23 1.42 1.42 1.42 1.42 1.52 1.37 1.22 1.20 1.40 1.20 1.25 1.45 1.22 1.52 1.32

10898938 10937523 10935698 10729345 10774100 10713873 10758033 10883797 10845397 10759465 10767278 10903965 10836352 10718598 10820280 10840477 10800629 10937800 10842472 10871417 10882530 10902418 10723555 10925452 10927207 10759459 10846962 10925371 10720518 10908227 10830161 10900073 10756268 10756270 10756272 10759445 10865347 10726672 10924669 10843845 10765036 10828841 10815955 10939061 10748763 10752799 10718134

List 7. Genes Expressed Differentially in Stressed F3-Control Rat Cortex Region as Compared to Non-Stressed F3-Control ('Str-Con vs Nst-Con' contrast), 290 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis Tnfaip8l1 XM_236787 -23 0.81 10931477 tumor necrosis factor, alpha-induced protein 8-like 1 Cell Cycle Ccne2 NM_001108656 -15 0.81 10867614 cyclin E2




15


Fcho2 RGD1562871 CytoskeletonECM Afap1

ENSRNOT00000020692 NM_001106935

-88 -15

0.82 0.83

10820770 10934664

FCH domain only 2 similar to BMI1-like protein

NM_080900

17

1.28

10777450

Capza1

NM_001109625

-143

0.82

10825686

Ceacam11 Cspg4 Cldn16 Emilin1 Gm52 Krtap4-7 Nvl Papln Pcdh19 RGD1564515 RGD1564955

NM_001025404 NM_031022 NM_131905 NM_001106710 NM_001014771 ENSRNOT00000068237 NM_001105980 NM_001108039 NM_001169129 ENSRNOT00000056894 ENSRNOT00000033044

9 -31 -7 -20 -27 -53 -44 -16 32 -10 7

1.26 0.77 0.82 0.82 0.78 0.69 0.78 0.81 1.21 0.80 1.23

10704634 10910237 10755027 10888953 10757808 10747166 10770351 10885823 10939226 10896803 10939640

RGD1309537 LOC290704 Smtnl1 Tpm2 Development Egln2 Fancl Fignl2

NM_001135017 ENSRNOT00000059673 ENSRNOT00000009903 NM_001024345

38 -9 19 18

1.26 0.79 1.21 1.23

10930421 10787918 10846862 10876324

actin filament associated protein 1 capping protein (actin filament) muscle Z-line, alpha 1 carcinoembryonic antigen-related cell adhesion molecule 11 chondroitin sulfate proteoglycan 4 claudin 16 elastin microfibril interfacer 1 envelope glycoprotein syncytin-A keratin associated protein 4-5 nuclear VCP-like papilin, proteoglycan-like sulfated glycoprotein protocadherin 19 similar to alpha 1B-glycoprotein similar to fibrous sheath interacting protein 2 similar to Myosin regulatory light chain 2-A, smooth muscle isoform (Myosin RLC-A) similar to palladin smoothelin-like 1 tropomyosin 2, beta

NM_001004083 ENSRNOT00000029513 ENSRNOT00000044982

59 -23 38

1.23 0.72 1.23

10719958 10774612 10907335

LOC681385

ENSRNOT00000067576

10

1.35

10843857

LOC685226 LOC687994 Olfml1

ENSRNOT00000045972 ENSRNOT00000030501 NM_001013192

60 -56 -85

1.67 0.83 0.75

10806527 10867109 10709687

Polr3k Retnlg Spata4 Sytl5

NM_001014259 NM_181625 NM_001002852 NM_178333

-186 10 6 22

0.77 1.22 1.22 1.21

10843132 10753861 10793083 10936877

Trpa1 Wbscr27 Electron Transport Cox6c1

NM_207608 NM_001109499

-9 -24

0.79 0.76

10867111 10761247

NM_173303

-22

0.78

10811879

Cyp2j3 Piwil2 Epigenetics As3mt Dmap1 Hist2h2bb Hist2h4 Hist3h2bb Hmgb2 Golgi

NM_175766 NM_001107276

27 -18

1.21 0.81

10878170 10785031

cytochrome c oxidase subunit VIc-1 cytochrome P450, family 2, subfamily j, polypeptide 3 piwi-like 2 (Drosophila)

NM_080890 NM_001015006 ENSRNOT00000042005 NM_001123469 NM_001109641 NM_017187

-12 -22 50 173 9 8

0.80 0.80 1.27 1.37 1.21 1.26

10715875 10938804 10817539 10825151 10742987 10791497

arsenic (+3 oxidation state) methyltransferase DNA methyltransferase 1-associated protein 1 histone cluster 2, H2bb histone cluster 2, H4 histone cluster 3, H2bb high mobility group box 2




16


EGL nine homolog 2 (C. elegans) Fanconi anemia, complementation group L fidgetin-like 2 similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4) similar to spermatogenesis associated glutamate (E)rich protein 4d similar to 82-kD FMRP Interacting Protein olfactomedin-like 1 polymerase (RNA) III (DNA directed) polypeptide K resistin-like gamma spermatogenesis associated 4 synaptotagmin-like 5 transient receptor potential cation channel, subfamily A, member 1 Williams Beuren syndrome chromosome region 27

Apparatus Rgp1 Growth Factors Amh Artn Edn2 Ccr9 Il18 Ing5 Hormones Pth Immune Response Obp3 C4bpa Ly6b Mup4 RT1-CE2 RT1-S2 Slamf9 Metabolism & Transport Aadacl2 Abhd1 Acot1 Akr1b7

ENSRNOT00000064419

53

1.21

10868541

RGP1 retrograde golgi transport homolog (S. cerevisiae)

NM_012902 NM_053397 NM_012549 NM_172329 NM_019165 NM_001108810

15 -14 -12 8 -16 -18

1.26 0.79 0.80 1.20 0.81 0.83

10900405 10879084 10871623 10914601 10909874 10925660

anti-Mullerian hormone artemin endothelin 2 chemokine (C-C motif) receptor 9 interleukin 18 inhibitor of growth family, member 5

NM_017044

14

1.25

10724987

parathyroid hormone

NM_147215 NM_012516 NM_139257 NM_198784 NM_001008840 NM_001008857 NM_001105971

9 -8 8 11 22 -21 -16

1.21 0.82 1.34 1.21 1.50 0.67 0.77

10877229 10767422 10904590 10877251 10831129 10827789 10765746

alpha-2u globulin PGCL4 complement component 4 binding protein, alpha lymphocyte antigen 6 complex, locus B major urinary protein 4 RT1 class I, locus CE2 RT1 class Ib, locus S2 SLAM family member 9

ENSRNOT00000067870 NM_001008520 NM_031315 NM_053781

7 54 6 9

1.25 1.28 1.24 1.31

10815616 10888931 10885857 10854427

Akr1d1 Apoa2 Apool Bphl Coq10b Dhrs7c Eno3 Fth1 Gnpnat1 Guf1 Gykl1 Klk1c10

NM_138884 NM_013112 NM_001014105 NM_001037206 NM_001009671 ENSRNOT00000036752 NM_012949 BC081845 NM_001134756 NM_001107215 NM_134341 NM_001135173

-15 -19 -26 16 -88 -8 15 -52 -82 -89 13 -22

0.78 0.82 0.79 1.28 0.76 0.79 1.23 0.76 0.80 0.82 1.31 0.74

10854548 10765530 10934700 10798100 10923338 10734701 10735331 10713831 10782846 10776646 10801717 10721283

Lrp1b Mgst1

NM_001107843 NM_134349

-207 28

0.79 1.25

10844988 10859392

Pigw Plch1 RGD1561057 RGD1561777 Scd4 Slc10a4 Proteolysis Adamtsl4

NM_194461 ENSRNOT00000013280 ENSRNOT00000043238 ENSRNOT00000035047 ENSRNOT00000017834 NM_001008555

-43 8 7 28 40 -20

0.83 1.21 1.23 1.28 1.20 0.79

10745782 10823432 10846671 10833617 10715552 10776582

arylacetamide deacetylase-like 2 abhydrolase domain containing 1 acyl-CoA thioesterase 1 aldo-keto reductase family 1, member B7 aldo-keto reductase family 1, member D1 (delta 4-3ketosteroid-5-beta-reductase) apolipoprotein A-II apolipoprotein O-like biphenyl hydrolase-like (serine hydrolase) coenzyme Q10 homolog B (S. cerevisiae) dehydrogenase enolase 3, beta, muscle ferritin, heavy polypeptide 1 glucosamine-phosphate N-acetyltransferase 1 GUF1 GTPase homolog (S. cerevisiae) glycerol kinase-like 1 T-kininogenase low density lipoprotein-related protein 1B (deleted in tumors) microsomal glutathione S-transferase 1 phosphatidylinositol glycan anchor biosynthesis, class W phospholipase C, eta 1 ceramide kinase-like similar to Na+ dependent glucose transporter 1 stearoyl-coenzyme A desaturase 4 solute carrier family 10 (sodium

NM_001034012

-13

0.78

10833985

Agt Hpn Pomp

NM_134432 NM_017112 NM_001100942

92 -12 43

1.34 0.82 1.28

10811900 10720891 10760041




17


ADAMTS-like 4 angiotensinogen (serpin peptidase inhibitor, clade A, member 8) hepsin proteasome maturation protein

Psmg4 Rnf113a1 Rnft1 Usp30 Receptors & Binding Proteins

NM_001129879 NM_001014791 ENSRNOT00000005064 NM_001107153

-17 -15 -93 44

0.82 0.82 0.81 1.26

10798096 10936285 10737380 10762857

Abca17 Acvr2b Gpr179

NM_001031637 NM_031554 ENSRNOT00000055427

8 10 -11

1.22 1.23 0.79

10741044 10914230 10746701

Lilrb3 Ly49i6 Mtnr1b Olr1060 Olr1297 Olr130 Olr1431 Olr1567 Olr1607 Olr1664 Olr222 Olr29 Olr315 Olr485 Olr551 Olr664 Olr703 Olr771 Olr813 Olr830 Olr855 Olr862 Olr905 Olr93 P2rx7 Prokr2 PVR V1rc28 V1rd6 Vom2r7 Vom2r-ps53 Signaling Akap14 Chka Frmpd1 Grtp1 Gna15 Gnas LOC689617

NM_031713 NM_001009718 NM_001100641 NM_001000698 NM_001000461 NM_001001272 NM_001000778 NM_001000043 NM_001000534 NM_001001007 NM_001000201 NM_001000691 NM_001000243 NM_001000307 NM_001000670 NM_001000347 NM_001000359 NM_001000610 NM_001000846 NM_001000900 NM_001000409 NM_001001071 NM_001001355 NM_001000141 NM_019256 NM_138978 NM_017076 NM_001009513 NM_001008923 NM_001099463 ENSRNOT00000012225

-12 8 -12 29 17 -13 -15 11 -21 8 -22 22 23 -8 -12 11 8 -22 -6 11 -9 -27 19 -20 -20 -16 -12 17 6 10 12

0.82 1.28 0.83 1.74 1.24 0.76 0.80 1.25 0.80 1.22 0.76 1.34 1.25 0.82 0.76 1.20 1.24 0.74 0.82 1.26 0.82 0.81 1.20 0.78 0.81 0.81 0.82 1.20 1.20 1.27 1.25

10703666 10866207 10915124 10900087 10916342 10724337 10733862 10752235 10779355 10795357 10724611 10723519 10712086 10846958 10847053 10837619 10847193 10838435 10855100 10858158 10871502 10879329 10893392 10724262 10761992 10850137 10719616 10855844 10703890 10703233 10719051

NM_021703 NM_017127 NM_001107937 ENSRNOT00000057740 NM_053542 NM_001159653 ENSRNOT00000058250

8 -48 25 -15 8 -7 64

1.24 0.83 1.23 0.82 1.20 0.83 1.63

10931995 10712706 10868693 10789500 10893474 10842657 10815215

Mnat1 Mrgprb4 Musk

NM_153472 ENSRNOT00000045792 NM_031061

-32 -42 -17

0.80 0.73 0.80

10885207 10722218 10869213




18


proteasome (prosome, macropain) assembly chaperone 4 ring finger protein 113A1 ring finger protein, transmembrane 1 ubiquitin specific peptidase 30

ATP-binding cassette, sub-family A (ABC1), member 17 activin A receptor, type IIB G protein-coupled receptor 179 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3 Ly49 inhibitory receptor 6 melatonin receptor 1B olfactory receptor 1060 olfactory receptor 1297 olfactory receptor 130 olfactory receptor 1431 olfactory receptor 1567 olfactory receptor 1607 olfactory receptor 1664 olfactory receptor 222 olfactory receptor 29 olfactory receptor 315 olfactory receptor 485 olfactory receptor 551 olfactory receptor 664 olfactory receptor 703 olfactory receptor 771 olfactory receptor 813 olfactory receptor 830 olfactory receptor 855 olfactory receptor 862 olfactory receptor 905 olfactory receptor 93 purinergic receptor P2X, ligand-gated ion channel, 7 prokineticin receptor 2 poliovirus receptor vomeronasal 1 receptor, C28 vomeronasal 1 receptor, D6 vomeronasal 2 receptor, 7 vomeronasal 2 receptor, pseudogene 53 A kinase (PRKA) anchor protein 14 choline kinase alpha FERM and PDZ domain containing 1 growth hormone regulated TBC protein 1 guanine nucleotide binding protein, alpha 15 GNAS complex locus similar to GTPase activating protein testicular GAP1 menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis) MAS-related GPR, member B4 muscle, skeletal, receptor tyrosine kinase

Pih1d1 RGD1561231 Socs6 Sppl2a Susd5 Transcription Bwk1 Cass4 Ccdc114 Ccdc153 Dmrta2 Duxbl Gtf2h4 Hoxd10 Hrasls Lmx1a

NM_001024868 ENSRNOT00000047232 ENSRNOT00000058179 NM_001107770 ENSRNOT00000028675

-14 12 -25 -110 -13

0.79 1.21 0.81 0.82 0.83

10706724 10795701 10805585 10849598 10913963

PIH1 domain containing 1 similar to MAP suppressor of cytokine signaling 6 signal peptide peptidase-like 2A sushi domain containing 5

NM_198743 ENSRNOT00000035245 NM_001126277 NM_001013953 NM_001107951 ENSRNOT00000052224 NM_212501 NM_001107094 NM_001105871 NM_001105967

-72 -13 -10 15 9 11 29 -28 31 -12

0.83 0.82 0.82 1.30 1.22 1.21 1.24 0.81 1.20 0.81

10842879 10842525 10707003 10909463 10870971 10786197 10827936 10837003 10754987 10765424

LOC499110 Nusap1 Rfx6

ENSRNOT00000041861 NM_001107762 NM_001106388

27 -10 12

1.21 0.81 1.21

10705431 10838843 10830105

RGD1563034 Srfbp1 RGD1564386 Zfp278 Znf295 Znf307 Ddx18 Translation & Protein Modification LOC681338 LOC683597 Mtrf1l RGD1564062 RGD1564552 Mrpl1 Rpl3 Rps9

ENSRNOT00000021187 NM_001005536 XM_001074961 NM_001107231 NM_001107105 ENSRNOT00000024797 NM_001006996

8 -27 8 9 -35 -20 -37

1.28 0.83 1.20 1.23 0.78 0.82 0.81

10719719 10801698 10824792 10773683 10753513 10798513 10767189

Bwk1 leukemia-related gene Cas scaffolding protein family member 4 coiled-coil domain containing 114 coiled-coil domain containing 153 DMRT-like family A2 double homeobox B-like general transcription factor II H, polypeptide 4 homeo box D10 HRAS-like suppressor LIM homeobox transcription factor 1 alpha similar to Zinc finger protein 354A (Transcription factor 17) (Renal transcription factor Kid-1) (Kidney, ischemia, and developmentally regulated protein 1) nucleolar and spindle associated protein 1 regulatory factor X, 6 similar to ETS domain transcription factor ERF (Ets2 repressor factor) serum response factor binding protein 1 similar to TDPOZ3 zinc finger protein 278 zinc finger protein 295 zinc finger protein 307 DEAD (Asp-Glu-Ala-Asp) box polypeptide 18

ENSRNOT00000047517 ENSRNOT00000030099 NM_001025723 ENSRNOT00000033738 ENSRNOT00000050803 NM_001105997 NM_198753 NM_031108

5 -9 -33 -48 -89 -52 203 184

1.24 0.83 0.82 0.76 0.72 0.83 1.27 1.26

10928032 10877637 10717785 10798841 10799888 10775719 10905530 10718510

Taf9 Miscellaneous & Unknown Fam133b LOC686013 LOC689425 LOC690206 LOC690422 LOC499542 Rwdd2a RGD1561161 RGD1565493 RGD1310587 RGD1562310 RGD1311269 RGD1308165

NM_001037310

-62

0.83

10812748

similar to ribosomal protein L31 similar to ribosomal protein L9 mitochondrial translational release factor 1-like similar to ribosomal protein L27a similar to ribosomal protein L21 mitochondrial ribosomal protein L1 ribosomal protein L3 ribosomal protein S9 TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor

BC094528 ENSRNOT00000007407 NM_001135002 NM_001109567 ENSRNOT00000029223 NM_001047943 NM_001108773 NM_001134510 XM_002729803 NM_001100857 NM_001109066 NR_033170 NM_001108664

-57 6 -16 -20 -10 9 -8 -11 -24 -19 16 28 -27

0.65 1.24 0.82 0.75 0.83 1.21 0.79 0.80 0.82 0.80 1.24 1.24 0.83

10936823 10810203 10828752 10873029 10887627 10821984 10912048 10813119 10903288 10770517 10762420 10928207 10868982

family with sequence similarity 133, member B hypothetical protein LOC686013 hypothetical protein LOC689425 hypothetical protein LOC690206 hypothetical protein LOC690422 LRRGT00178 RWD domain containing 2A similar to BC067074 protein similar to DKFZP434I092 protein similar to hypothetical protein FLJ14146 similar to hypothetical protein FLJ21415 similar to hypothetical protein FLJ37953 similar to hypothetical protein MGC17337




19


RGD1562039 RGD1563945

ENSRNOT00000049790 ENSRNOT00000061140

30 -21

1.21 0.82

10939072 10936645

RGD1560291 LOC501427 Samd12 Ttc36 Tmco5a Tmem156

XM_001078928 ENSRNOT00000061060 NM_001130562 NM_001005546 ENSRNOT00000006809 NM_001025138

-13 -12 -85 -38 11 9

0.81 0.77 0.81 0.77 1.22 1.25

10901121 10779531 10903721 10916876 10838571 10772760

Utp23 ESTs

NM_001126266

-23

0.82

10896499

MGC94199 RGD1308251

BC079168 NM_001108697 XR_009246 XR_008340 XR_008339 XR_008033 XR_007931 XR_007585 XR_007179 XR_007098 XR_006082 XR_006046 XR_005716 XM_001074777 ENSRNOT00000056786 ENSRNOT00000055830 ENSRNOT00000042423 ENSRNOT00000002166 AF272707

-64 44 17 -68 -56 -7 -50 35 -25 -37 6 -35 23 -170 -124 22 31 -5 34

0.80 1.26 1.40 0.71 0.60 0.79 0.78 1.56 0.78 0.62 1.25 0.75 1.58 0.73 0.54 1.34 1.27 0.82 1.45

10867596 10882071 10731555 10717829 10845365 10796881 10836964 10934560 10830126 10707370 10934692 10703137 10875005 10721276 10939699 10859174 10938712 10836988 10867318

ENSRNOT00000009117 ---------------------------------------------

-13 -173 -141 -130 -106 -93 -84 -80 -79 -73 -69 -66 -64 -64 -52 -47 -44 -41 -39 -38 -38 -27 -25

0.77 0.83 0.76 0.70 0.66 0.73 0.64 0.83 0.77 0.79 0.80 0.78 0.82 0.59 0.77 0.81 0.82 0.67 0.80 0.61 0.73 0.80 0.79

10867916 10732837 10805311 10742507 10827665 10848956 10903520 10768364 10798921 10934980 10810417 10817114 10833808 10914009 10723231 10932054 10716630 10830161 10914901 10866205 10795400 10877992 10818137




20


similar to MGC82337 protein similar to mKIAA0215 protein similar to NACHT, leucine rich repeat and PYD containing 4A similar to Spetex-2F protein sterile alpha motif domain containing 12 tetratricopeptide repeat domain 36 transmembrane and coiled-coil domains 5A transmembrane protein 156 UTP23, small subunit (SSU) processome component, homolog (yeast) similar to RIKEN cDNA 2610301B20; EST AI428449 similar to RIKEN cDNA 2810405K02

-----------------------------------------------------------------------------------------------------------------




-19 -19 -18 -17 -16 -15 -15 -14 -12 -11 -11 -10 -10 -9 -8 -6 6 6 7 8 8 9 9 9 9 9 9 9 10 10 10 10 11 11 13 14 15 16 17 19 19 19 22 24 25 26 27 27 29 29 29 31 35 44 50 57

0.79 0.78 0.77 0.65 0.76 0.76 0.77 0.78 0.82 0.76 0.79 0.82 0.77 0.75 0.76 0.82 1.20 1.20 1.25 1.24 1.24 1.33 1.23 1.26 1.30 1.22 1.24 1.26 1.41 1.26 1.34 1.44 1.31 1.27 1.37 1.29 1.32 1.38 1.21 1.25 1.37 1.26 1.35 1.38 1.37 1.33 1.41 1.78 1.26 1.27 1.29 1.31 1.30 1.43 1.98 1.57

10840363 10713011 10724240 10873723 10732217 10725541 10925371 10824526 10892481 10706465 10727600 10802574 10927158 10740841 10706238 10901139 10856127 10833090 10856177 10789696 10719036 10778804 10862942 10711995 10899717 10787805 10882530 10938066 10798792 10785598 10702317 10891491 10781995 10782889 10759597 10887052 10852413 10847172 10704147 10887066 10814299 10816483 10755550 10917344 10809067 10750898 10903965 10932699 10878640 10730659 10751799 10909137 10888388 10914898 10767278 10713873

21


-----

84 84

1.58 1.78

10934710 10856228

List 8. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat Cortex Region as Compared to NonStressed F3-Vinclozolin ('Str-Vin vs Nst-Vin' contrast), 96 genes and EST's Mean _diff

Ratio

Affymetrix ID

NM_080394

-67

0.81

10853020

RGD1563738 Epigenetics LOC501799 Growth Factors Ctgf Fgf9 Immune Response Btnl4 Metabolism & Transport Acot1

ENSRNOT00000052026

17

1.34

10916270

reelin similar to Discs, large homolog 5 (Placenta and prostate DLG)

ENSRNOT00000061397

107

1.75

10759485

similar to chromobox homolog 3

NM_022266 NM_012952

43 -80

1.28 0.81

10717233 10780813

connective tissue growth factor fibroblast growth factor 9

NM_001166344

7

1.27

10828340

butyrophilin-like 4

NM_031315

5

1.20

10885857

Slc32a1 Lrp12 Pcbd1

NM_031782 NM_001134883 NM_001007601

-78 -81 -16

0.80 0.82 0.82

10841774 10903503 10830003

Piga

NM_001108816

45

1.20

10937719

Pla2g7 Proteolysis Ube2n Receptors & Binding Proteins Ddr2 Igfbp6 Olr1559 Olr213 Olr756 Olr862 LOC304239 Vom2r1 Vom2r2 Signaling RGD1560808 RGD1560825 RGD1561667 RGD1564858 RGD1565231 Transcription

NM_001009353

56

1.21

10926683

acyl-CoA thioesterase 1 solute carrier family 32 (GABA vesicular transporter), member 1 low density lipoprotein-related protein 12 pterin-4 alpha-carbinolamine dehydratase phosphatidylinositol glycan anchor biosynthesis, class A phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)

BC090072

33

1.58

10759435

ubiquitin-conjugating enzyme E2N

NM_031764 NM_013104 NM_001000049 NM_001000735 NM_001000614 NM_001001071 ENSRNOT00000049215 NM_001099460 ENSRNOT00000051591

-17 -78 -16 14 -9 -24 26 20 9

0.78 0.68 0.83 1.25 0.79 0.82 1.40 1.21 1.25

10769695 10899465 10750647 10724601 10838414 10879329 10834046 10701668 10701636

discoidin domain receptor tyrosine kinase 2 insulin-like growth factor binding protein 6 olfactory receptor 1559 olfactory receptor 213 olfactory receptor 756 olfactory receptor 862 similar to RalA binding protein 1 vomeronasal 2 receptor, 3 vomeronasal 2 receptor, 2

ENSRNOT00000048991 ENSRNOT00000059958 ENSRNOT00000059957 ENSRNOT00000047604 ENSRNOT00000065348

29 22 17 15 25

1.35 1.25 1.25 1.23 1.24

10718191 10703256 10703287 10703274 10718188

similar to putative protein kinase similar to putative protein kinase similar to putative protein kinase similar to putative protein kinase similar to putative protein kinase

Chchd2 Klhl20 Med21

NM_001015019 NM_001107192 NM_001107895

-99 -46 -46

0.79 0.80 0.83

10930091 10769204 10859655

coiled-coil-helix-coiled-coil-helix domain containing 2 kelch-like 20 (Drosophila) mediator complex subunit 21

Gene Symbol Development Reln




GenBank_Reference Sequence

22


Gene Title

RGD1560135 RGD1563747 RGD1565550 Txnip Zcchc5 Translation & Protein Modification Mrpl45 Rnaseh2b RGD1564095 RGD1565170 RGD1559877 RGD1564552 Miscellaneous & Unknown LOC498544 Spetex-2A Mir196a EST's RGD1559459




ENSRNOT00000040584 ENSRNOT00000040887 ENSRNOT00000040584 NM_001008767 ENSRNOT00000003296

27 29 36 142 -14

1.23 1.25 1.26 1.37 0.83

10830272 10833468 10830279 10817552 10938988

similar to double homeobox, 4 similar to double homeobox, 4 similar to double homeobox, 4 thioredoxin interacting protein zinc finger, CCHC domain containing 5

NM_001105834 NM_001007007 ENSRNOT00000061899 ENSRNOT00000043836 ENSRNOT00000049689 ENSRNOT00000050803

-53 -34 21 -16 23 -37

0.83 0.80 1.28 0.73 1.39 0.83

10737815 10780937 10867377 10780763 10800511 10799888

mitochondrial ribosomal protein L45 ribonuclease H2, subunit B similar to 60S acidic ribosomal protein P2 similar to 60S ribosomal protein L23a similar to 60S ribosomal protein L29 (P23) similar to ribosomal protein L21

AY383688 ENSRNOT00000061476 NR_031913

9 14 8

1.20 1.29 1.24

10702078 10782777 10899597

hypothetical protein LOC498544 Spetex-2B protein microRNA mir-196a

ENSRNOT00000065079 XR_008286 XR_008099 XR_007963 XR_007931 NC_001665 ENSRNOT00000054517 ENSRNOT00000053929 ENSRNOT00000053328 ENSRNOT00000053279 ENSRNOT00000053042 ENSRNOT00000052710 ENSRNOT00000052661 ENSRNOT00000052661 ENSRNOT00000052507 ENSRNOT00000048364 ENSRNOT00000006888 AF188753 ENSRNOT00000039948 -----------------------------------

-5 -23 -50 16 -33 -282 -70 113 -180 -241 78 -107 -739 -739 -802 -12 22 -209 32 55 -1073 -829 -620 -596 -545 -381 -236 -190 -165 -103 -98 -48 -32 -21 -11 8

0.80 0.75 0.82 1.25 0.83 0.62 0.64 1.35 0.72 0.80 1.64 0.64 0.73 0.73 0.68 0.77 1.22 0.76 1.28 1.23 0.46 0.76 0.61 0.76 0.70 0.76 0.56 0.59 0.78 0.82 0.73 0.82 0.81 0.77 0.81 1.22

10771998 10934032 10798900 10903522 10836964 10930569 10797013 10839872 10855946 10708691 10937568 10838282 10722437 10722441 10722471 10900112 10892493 10855185 10767044 10748601 10722449 10761253 10722481 10722461 10722433 10758031 10722451 10722427 10848027 10846928 10722459 10787706 10884738 10831804 10894798 10850313

similar to Expressed sequence AI788959

23


-----------------------------

9 12 12 14 14 25 26 29 33 33 33 33 56 72

1.23 1.21 1.34 1.32 1.32 1.20 1.20 1.31 1.58 1.58 1.58 1.58 1.31 1.51

10860595 10714183 10769229 10785598 10774339 10771525 10888388 10734368 10756268 10756270 10756272 10759445 10934710 10933038

List 9. Genes Expressed Differentially in Non-Stressed F3-Vinclozolin Rat CA1 of the Hippocampus as Compared to NonStressed F3-Control ('Nst-Vin vs Nst-Con' contrast), 68 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis Ankdd1a ENSRNOT00000033512 16 1.29 10918281 ankyrin repeat and death domain containing 1A RGD1563348 NM_001114939 13 1.30 10912076 similar to Selenoprotein H RGD1559610 BC168964 73 1.21 10879679 similar to CGI-94 protein CytoskeletonECM Gpc4 NM_001014108 65 1.32 10939744 glypican 4 Kb23 NM_001008813 33 1.21 10907369 type II keratin Kb23 Pcdh8 NM_022868 49 1.24 10785461 protocadherin 8 Pcdhb19 ENSRNOT00000060484 40 1.27 10801204 protocadherin beta 19 Rimbp2 NM_001100488 82 1.25 10758064 RIMS binding protein 2 Scg3 NM_053856 196 1.20 10918738 secretogranin III Epigenetics dapper, antagonist of beta-catenin, homolog 3 Dact3 ENSRNOT00000043203 69 1.20 10704555 (Xenopus laevis) Immune Response complement component 1, q subcomponent binding C1qbp NM_019259 84 1.20 10744568 protein C1ql3 NM_001109403 235 1.42 10799733 complement component 1, q subcomponent-like 3 Metabolism & Transport Atp11a NM_001107324 -213 0.72 10792859 ATPase, class VI, type 11A Car14 NM_001109655 -118 0.62 10825100 carbonic anhydrase 14 Chi3l4 ENSRNOT00000055968 7 1.20 10825770 chitinase 3-like 4 Lrp12 NM_001134883 114 1.24 10903501 low density lipoprotein-related protein 12 Slc8a2 NM_078619 163 1.24 10704437 solute carrier family 8 (sodium Retsat NM_145084 166 1.36 10856424 retinol saturase (all trans retinol 13,14 reductase) Sulf1 NM_134378 -67 0.71 10874981 sulfatase 1 Proteolysis Rnf213 ENSRNOT00000004904 -16 0.82 10740016 ring finger protein 213 Receptors & Binding Proteins Olr1320 NM_001000471 19 1.28 10909285 olfactory receptor 1320 Olr1424 NM_001000779 10 1.24 10742937 olfactory receptor 1424 Olr221 NM_001000200 -13 0.82 10724609 olfactory receptor 221 Olr711 NM_001000625 -6 0.83 10847213 olfactory receptor 711




24


Signaling Calcoco2 Akap5 Defb42 Enpp2

XM_220903 NM_133515 NM_001037532 NM_057104

6 71 -151 -2109

1.24 1.20 0.83 0.42

10746588 10885393 10784446 10903736

calcium binding and coiled-coil domain 2 A kinase (PRKA) anchor protein 5 defensin beta 42 ectonucleotide pyrophosphatase pleckstrin homology domain containing, family O member 2 ProSAPiP1 protein Rab40b, member RAS oncogene family similar to diacylglycerol kinase eta SMAD family member 1 sphingomyelin phosphodiesterase, acid-like 3B

Plekho2 Prosapip1 Rab40b RGD1561955 Smad1 Smpdl3b Transcription Bhlhe41 Baz1b Casc5 Ccdc34 Dnajc8 Kbtbd11 Klhl12 Mitf

ENSRNOT00000042633 NM_172022 NM_001107076 ENSRNOT00000058079 NM_013130 NM_001025737

27 130 63 93 38 55

1.22 1.23 1.20 1.35 1.24 1.28

10918288 10849927 10749809 10785405 10806981 10880339

AF009329 ENSRNOT00000001975 ENSRNOT00000067081 NM_001108587 NM_001013168 NM_001107326 NM_153730 ENSRNOT00000051121

102 77 51 29 148 42 44 -22

1.29 1.20 1.40 1.21 1.21 1.33 1.22 0.81

10867026 10761209 10838741 10838373 10880372 10792660 10764126 10857435

LOC691642

XM_002726878

19

1.27

10894417

LOC680767 Translation & Protein Modification RGD1559743 Miscellaneous & Unknown

ENSRNOT00000060096

133

1.22

10760816

basic helix-loop-helix family, member e41 bromodomain adjacent to zinc finger domain, 1B cancer susceptibility candidate 5 coiled-coil domain containing 34 DnaJ (Hsp40) homolog, subfamily C, member 8 kelch repeat and BTB (POZ) domain containing 11 kelch-like 12 (Drosophila) microphthalmia-associated transcription factor similar to high mobility group nucleosomal binding domain 1 similar to transcription elongation factor B (SIII), polypeptide 1

XM_001077121

-21

0.82

10920785

similar to 40S ribosomal protein S16

Utp18 RGD1308601 EST's

NM_001135039 NM_001107374

58 63

1.22 1.24

10746256 10805304

UTP18, small subunit (SSU) processome component, homolog (yeast) similar to hypothetical protein

-164 -108 -58 -48 -46 -45 -41 -40 -27 -15 -15 -12 7 10 11 14 14 17 18 23 74

0.82 0.71 0.83 0.81 0.78 0.82 0.76 0.75 0.82 0.82 0.82 0.83 1.23 1.25 1.36 1.22 1.25 1.23 1.21 1.23 1.26

10750114 10716702 10740505 10923727 10830161 10820145 10892648 10788099 10932580 10887022 10887038 10787822 10823674 10722713 10850319 10707254 10749852 10827347 10804461 10887336 10809882

-------------------------------------------




25


List 10. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat CA1 of the Hippocampus as Compared to Stressed F3-Control ('St-Vin vs St-Con' contrast), 155 genes and EST's 
 GenBank_Reference Sequence

Mean _diff

Ratio

Affymetrix ID

Tnfsf4 Tnfaip8l3 Cell Cycle Cspp1 CytoskeletonECM Bgn

NM_053552 ENSRNOT00000038830

-24 -10

0.79 0.80

10765092 10917501

tumor necrosis factor (ligand) superfamily, member 4 tumor necrosis factor, alpha-induced protein 8-like 3

ENSRNOT00000030345

-84

0.79

10875091

centrosome and spindle pole associated protein 1

NM_017087

48

1.38

10935890

Ceacam10 Myom2 LOC680489

NM_173339 NM_001169141 NM_001109415

9 -9 -19

1.28 0.83 0.81

10705034 10792621 10938099

Twf1 Development Auts2 Nlgn1 Syt17 Sntg1 Tert Tor1b Vgll3 Electron Transport

NM_001008521

9

1.22

10871693

biglycan carcinoembryonic antigen-related cell adhesion molecule 10 myomesin 2 similar to claudin 1 twinfilin, actin-binding protein, homolog 1 (Drosophila)

ENSRNOT00000044800 NM_053868 NM_138849 ENSRNOT00000009679 NM_053423 NM_001039197 ENSRNOT00000042316

-42 -86 203 -71 -18 39 -37

0.81 0.83 1.26 0.83 0.83 1.25 0.74

10761299 10822545 10725235 10867345 10717517 10835261 10749839

autism susceptibility candidate 2 neuroligin 1 synaptotagmin XVII syntrophin, gamma 1 telomerase reverse transcriptase torsin family 1, member B vestigial like 3 (Drosophila)

Cyp2c13

NM_138514

-32

0.82

10930762

cytochrome P450, family 2, subfamily c, polypeptide 13

LOC100174910 Epigenetics Brd8 Growth Factors Gdf10 Gdf9 Il15 Kng1l1 LOC360228 Sept12 Tgfb2 Immune Response Il22 LOC688858 RT1-DMb RT1-M6-1 Metabolism & Transport Dio2

NM_001131003

-90

0.78

10804552

glutaredoxin-like protein

NM_001008509

57

1.22

10803774

bromodomain containing 8

NM_024375 NM_021672 NM_013129 NM_001009628 NM_001003706 NM_001100865 NM_031131

-25 41 -15 -49 -25 -11 150

0.76 1.23 0.82 0.72 0.80 0.81 1.37

10786905 10733506 10806899 10755135 10736875 10731699 10770577

growth differentiation factor 10 growth differentiation factor 9 interleukin 15 kininogen 1-like 1 WDNM1 homolog septin 12 transforming growth factor, beta 2

ENSRNOT00000009776 XM_001068599 NM_198740 NM_001008852

-15 -181 37 -45

0.82 0.82 1.26 0.74

10895618 10759581 10831620 10827686

interleukin 22 similar to CD209a antigen RT1 class II, locus DMb RT1 class I, locus M6, gene 1

NM_031720

24

1.22

10891402

Ddost Mocos

NM_001012104 NM_001108425

234 -12

1.22 0.82

10873303 10800546

deiodinase, iodothyronine, type II dolichyl-diphosphooligosaccharide-protein glycosyltransferase molybdenum cofactor sulfurase

Gene Symbol

Gene Title

Apoptosis




26


Por Ppid RGD1565145 Ttpal Proteolysis Klk15 LOC688812 Pm20d2 Prcp Ubc Ubd Receptors & Binding Proteins Gfra1 Ifngr1 LOC304239 Olr1057 Olr1405 Olr160 Olr1734 Olr542 Olr582 Olr584 Olr629 Olr720 Olr734 Olr996 Paqr5 Robo3 Tlr2 Vom2r66 Vom2r-ps27 Signaling Ebag9 Gbp4

NM_031576 NM_001004279 ENSRNOT00000017696 NM_001106537

73 -243 -12 61

1.21 0.83 0.80 1.22

10761162 10816008 10914045 10842032

P450 (cytochrome) oxidoreductase peptidylprolyl isomerase D (cyclophilin D) similar to cysteine sulfinic acid decarboxylase tocopherol (alpha) transfer protein-like

ENSRNOT00000038353 XR_085983 NM_001107922 NM_001106281 NM_017314 NM_053299

-16 -31 16 91 284 -31

0.83 0.79 1.23 1.32 1.26 0.83

10706498 10756117 10875853 10708672 10758134 10830854

kallikrein-related peptidase 15 similar to ubiquitin-activating enzyme E1C peptidase M20 domain containing 2 prolylcarboxypeptidase (angiotensinase C) ubiquitin C ubiquitin D

NM_012959 NM_053783 ENSRNOT00000049215 NM_001000072 NM_001001012 NM_001000738 NM_001001119 NM_001000566 NM_001000662 NM_001000661 NM_001001058 NM_001001067 NM_001000617 NM_001000700 NM_001014092 NM_001108135 NM_198769 ENSRNOT00000051621 ENSRNOT00000051051

92 96 -45 -14 -31 -23 -8 -30 -35 -13 -24 -26 -22 30 21 -15 10 66 -17

1.30 1.22 0.72 0.83 0.82 0.81 0.76 0.70 0.67 0.83 0.76 0.82 0.81 1.37 1.21 0.81 1.26 1.32 0.83

10731075 10701924 10756334 10900081 10733296 10709507 10827639 10847042 10837545 10847074 10847109 10847229 10847242 10893375 10918055 10916201 10823970 10774903 10718403

GDNF family receptor alpha 1 interferon gamma receptor 1 similar to RalA binding protein 1 olfactory receptor 1057 olfactory receptor 1405 olfactory receptor 160 olfactory receptor 1734 olfactory receptor 542 olfactory receptor 582 olfactory receptor 584 olfactory receptor 629 olfactory receptor 720 olfactory receptor 734 olfactory receptor 996 progestin and adipoQ receptor family member V roundabout homolog 3 (Drosophila) toll-like receptor 2 vomeronasal 2 receptor, 66 vomeronasal 2 receptor, pseudogene 27

NM_001009665 ENSRNOT00000022648

77 -12

1.20 0.83

10896486 10819512

Smek1 Sh3bp4 Transcription Ccdc37 Dnajc11 Dnajc30 Elk1 Gtf2ird1 Hint1 Luzp1 Ldoc1l

NM_001108050 NM_022693

94 105

1.21 1.38

10891719 10925264

estrogen receptor binding site associated, antigen, 9 guanylate binding protein 4 SMEK homolog 1, suppressor of mek1 (Dictyostelium) SH3-domain binding protein 4

ENSRNOT00000024222 NM_001108694 NM_001109024 NM_001108059 NM_001001504 ENSRNOT00000006471 AF181259 ENSRNOT00000039588

-15 83 21 72 -16 -13 -16 83

0.76 1.21 1.30 1.22 0.82 0.78 0.83 1.29

10864025 10874223 10761225 10936520 10757829 10862836 10873012 10905915

LOC691468 Tdpoz1

XM_002724499 XM_345239

42 40

1.22 1.20

10733914 10824790

Tada2b Zfp212 Znf307 Znf488

NM_001170455 ENSRNOT00000009054 ENSRNOT00000024797 ENSRNOT00000031496

-44 -64 -31 13

0.81 0.83 0.81 1.24

10773358 10855203 10795315 10790433




27


coiled-coil domain containing 37 DnaJ (Hsp40) homolog, subfamily C, member 11 DnaJ (Hsp40) homolog, subfamily C, member 30 ELK1, member of ETS oncogene family GTF2I repeat domain containing 1 histidine triad nucleotide binding protein 1 leucine zipper protein 1 leucine zipper, down-regulated in cancer 1-like similar to Zinc finger protein 84 (Zinc finger protein HPF2) TD and POZ domain containing 1 transcriptional adaptor 2 (ADA2 homolog, yeast)beta Zinc finger protein 212 zinc finger protein 307 zinc finger protein 488

Translation & Protein Modification LOC362863 Ptrh1 Polr1b Rplp2 RGD1563551 Miscellaneous & Unknown LOC100192313 LOC502684 LOC691649 Rcan3 RGD1564171 RGD1311188 MGC94282 RGD1564129 RGD1563072 Ttc21a Tsku EST's RGD1311575 RGD1306462 RGD1306446




NM_001170605 NM_001108580 NM_031773 NM_001030021 ENSRNOT00000047507

-13 -23 37 367 -7

0.83 0.82 1.22 1.24 0.79

10894643 10835624 10839751 10776809 10865372

first gene upstream of Nt5dc3 peptidyl-tRNA hydrolase 1 homolog (S. cerevisiae) polymerase (RNA) I polypeptide B ribosomal protein, large P2 similar to ribosomal protein L31

NM_001136261 NM_001025060 ENSRNOT00000005237 NM_001012746 NM_001109186 BC162017 NR_027366 ENSRNOT00000038189 NM_001107981 ENSRNOT00000043831 NM_001009965

250 -12 110 33 -35 44 20 -7 58 -13 -33

1.20 0.76 1.23 1.32 0.72 1.21 1.28 0.83 1.23 0.79 0.81

10902333 10840826 10734061 10880610 10816879 10897118 10865838 10795611 10872059 10914271 10723822

hypothetical protein LOC100192313 hypothetical protein LOC502684 hypothetical protein LOC691649 RCAN family member 3 RGD1564171 similar to 1500031N24Rik protein similar to 5930416I19Rik protein similar to hypothetical protein 4930474N05 similar to hypothetical protein FLJ38984 tetratricopeptide repeat domain 21A tsukushin

ENSRNOT00000002908 BC097453 NM_001008554 -------------------------------------------------------------

-32 -13 -9 -202 -126 -75 -64 -57 -51 -49 -44 -44 -41 -39 -37 -35 -35 -33 -30 -29 -28 -28 -27 -27 -26 -26 -25 -21 -21 -20 -18 -15 -14

0.81 0.83 0.82 0.79 0.80 0.82 0.74 0.80 0.78 0.79 0.81 0.70 0.68 0.82 0.78 0.77 0.81 0.76 0.77 0.70 0.81 0.54 0.76 0.77 0.66 0.61 0.79 0.77 0.78 0.78 0.65 0.82 0.75

10776361 10906065 10772030 10855185 10932269 10890648 10831148 10894227 10872129 10788314 10914901 10807957 10818911 10820213 10804712 10796438 10746789 10883023 10914877 10840477 10717953 10736193 10790465 10726483 10723687 10776289 10893305 10802574 10755550 10771204 10807883 10850090 10877567

hypothetical LOC289568 similar to RIKEN cDNA 1700019P01 similar to RIKEN cDNA 9930032O22 gene

28


-------------------------------------------------------

-13 -12 -12 -11 -11 -10 -10 -10 -9 -8 -8 -8 -8 -7 5 8 9 12 13 22 27 31 32 42 46 68 111

0.75 0.82 0.78 0.81 0.83 0.80 0.79 0.82 0.80 0.76 0.79 0.83 0.81 0.82 1.21 1.20 1.22 1.32 1.24 1.59 1.21 1.35 1.22 1.21 1.24 1.60 1.22

10701666 10725517 10830185 10894874 10764047 10763316 10890166 10754929 10803721 10933227 10729120 10839972 10776737 10863051 10814661 10877368 10894850 10886244 10823498 10850319 10764400 10934042 10896201 10880526 10797939 10722816 10708560

List 11. Genes Expressed Differentially in Stressed F3-Control Rat CA1 of the Hippocampus as Compared to Non-Stressed F3-Control ('Str-Con vs Nst-Con' contrast), 118 genes and EST's Mean _diff

Ratio

Affymetrix ID

NM_012794 NM_001008813 NM_198050 NM_012974

-65 32 -20 -44

0.79 1.20 0.78 0.78

10907749 10907369 10793846 10793140

Lpp Development Atn1 Pbxip1 Pinx1 Rex2 Rhox11 Electron Transport Cox8b Etfb Prdx4 Pet112l Tmem126a Epigenetics

NM_001013864

-34

0.78

10755069

glycosylation dependent cell adhesion molecule 1 type II keratin Kb23 kinesin family member 27 laminin, beta 2 LIM domain containing preferred translocation partner in lipoma

NM_017228 NM_001100976 NM_001083337 ENSRNOT00000040918 NM_001024873

57 -51 -24 52 13

1.22 0.79 0.80 1.28 1.25

10865487 10816807 10781014 10873880 10936270

atrophin 1 pre-B-cell leukemia homeobox interacting protein 1 PIN2-interacting protein 1 reduced expression 2 reproductive homeobox 11

NM_012786 NM_001004220 NM_053512 ENSRNOT00000057128 NM_001011557

-10 -65 -40 -64 -30

0.81 0.81 0.82 0.82 0.81

10726669 10706339 10933699 10816176 10723639

cytochrome c oxidase, subunit VIIIb electron-transfer-flavoprotein, beta polypeptide peroxiredoxin 4 PET112-like (yeast) transmembrane protein 126A

Cbfa2t3

NM_001108453

12

1.21

10811688

core-binding factor, runt domain, alpha subunit 2; translocated to, 3

Gene Symbol CytoskeletonECM Glycam1 Kb23 Kif27 Lamb2




GenBank_Reference Sequence

29


Gene Title

Growth Factors Igf2r Mif Immune Response Mr1 LOC287167 Metabolism & Transport Acaa2 Aldh2 Apoc1

NM_012756 NM_031051

-91 -270

0.80 0.83

10702996 10829649

insulin-like growth factor 2 receptor macrophage migration inhibitory factor

NM_001100635 NM_001013853

-23 -93

0.82 0.78

10768819 10741765

major histocompatibility complex, class I-related globin, alpha

NM_130433 NM_032416 NM_012824

-46 -87 -26

0.80 0.76 0.74

10802691 10758663 10719524

Atp5g1

NM_017311

-134

0.83

10746583

Atp5g2 Decr1 Grhpr Gsta3 Gsta4 Hba-a2 Hbb Idh2

NM_133556 NM_057197 NM_001113754 NM_031509 NM_001106840 NM_013096 NM_033234 NM_001014161

-180 -53 -50 -304 -29 -1385 -300 -129

0.82 0.83 0.83 0.81 0.69 0.63 0.64 0.74

10907634 10875631 10868673 10926958 10911797 10741756 10724311 10723020

LOC682386 Ndufab1 Odc1 Pex14 Prodh

ENSRNOT00000027244 NM_001106294 NM_012615 NM_172063 NM_001135778

-37 -209 -137 50 -122

0.80 0.77 0.82 1.27 0.75

10803759 10725474 10883785 10881648 10752352

Sult1a1 Tcn2 Urod Proteolysis Rnf213 Cst3 Mcpt4l1 LOC688812 Receptors & Binding Proteins

NM_031834 NM_022534 NM_019209

-60 -127 -74

0.78 0.74 0.82

10725782 10778028 10878926

acetyl-Coenzyme A acyltransferase 2 aldehyde dehydrogenase 2 family (mitochondrial) apolipoprotein C-I ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9) ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9) 2,4-dienoyl CoA reductase 1, mitochondrial glyoxylate reductase glutathione S-transferase A3 glutathione S-transferase alpha 4 hemoglobin alpha, adult chain 2 hemoglobin, beta isocitrate dehydrogenase 2 (NADP+), mitochondrial similar to Nucleoside diphosphate kinase homolog 5 (NDK-H 5) (NDP kinase homolog 5) (nm23-M5) NADH dehydrogenase (ubiquinone) 1, alpha ornithine decarboxylase 1 peroxisomal biogenesis factor 14 proline dehydrogenase sulfotransferase family, cytosolic, 1A, phenolpreferring, member 1 transcobalamin 2 uroporphyrinogen decarboxylase

ENSRNOT00000004904 NM_012837 XM_001056983 XR_085983

-16 -809 11 26

0.81 0.83 1.21 1.22

10740016 10850563 10780538 10756117

ring finger protein 213 cystatin C mast cell protease 4-like 1 similar to ubiquitin-activating enzyme E1C

LOC100363058 Mt2A Mt2A Olr1320 Olr567 Olr760 Vom2r-ps27 Signaling Ctnnal1 Dusp5 Fkbp14 Fxyd1 Mark2 Magmas

XM_002742441 NM_001137564 NM_001137564 NM_001000471 NM_001000326 NM_001001069 ENSRNOT00000051051

-17 -171 -326 16 -12 28 17

0.79 0.78 0.81 1.24 0.82 1.33 1.21

10709757 10827989 10809399 10909285 10847060 10848105 10718403

olfactory receptor 480-like metallothionein 2A metallothionein 2A olfactory receptor 1320 olfactory receptor 567 olfactory receptor 760 vomeronasal 2 receptor, pseudogene 27

NM_001106649 NM_133578 NM_001013210 NM_031648 NM_021699 NM_001100136

-78 -28 -66 -261 98 -24

0.77 0.77 0.75 0.80 1.22 0.83

10876896 10716080 10862643 10720878 10728396 10731783

catenin (cadherin associated protein), alpha-like 1 dual specificity phosphatase 5 FK506 binding protein 14 FXYD domain-containing ion transport regulator 1 MAP mitochondria-associated protein involved in




30


granulocyte-macrophage colony-stimulating factor signal transduction NIMA (never in mitosis gene a)-related kinase 6

Nek6 Transcription E2f5

NM_182953

-38

0.83

10835964

ENSRNOT00000014361

-22

0.75

10718609

Giot1 Id3

NM_133563 NM_013058

68 -49

1.25 0.83

10900841 10872972

Polr3k Zcchc11 Translation & Protein Modification Mrpl54

NM_001014259 NM_001107953

-158 54

0.82 1.20

10843132 10870777

NM_001106770

-102

0.79

10893586

Mphosph10

NM_001106340

40

1.21

10722566

LOC499485 RGD1563579 Serp1 Miscellaneous & Unknown Fam100a

XM_002725892 ENSRNOT00000057412 NM_030835

22 15 -201

1.23 1.20 0.80

10820047 10939086 10823309

mitochondrial ribosomal protein L54 M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein) similar to 60S ribosomal protein L17 (L23) (Amino acid starvation-induced protein) (ASI) similar to 60S ribosomal protein L29 (P23) stress-associated endoplasmic reticulum protein 1

77

1.20

10731734

family with sequence similarity 100, member A

LOC100364350 RGD1562420 RGD1560187 RGD1561667 Tmem147 Tmem38b EST's RGD1311378

XM_002725175 ENSRNOT00000007683 NM_001173556 XM_217999 NM_001038494 NM_001014191

-64 44 -140 16 -41 -37

0.81 1.39 0.83 1.23 0.83 0.78

10790658 10887809 10880897 10703216 10720767 10869151

NACHT and WD repeat domain containing 1-like similar to hypothetical protein similar to Hypothetical UPF0327 protein similar to putative protein kinase transmembrane protein 147 transmembrane protein 38B

BC166836 -------------------------------------------------

-42 -81 -56 -49 -31 -28 -28 -26 -26 -22 -22 -21 -18 -12 -9 -9 13 13 14 17 19 23 25 28 29

0.83 0.78 0.83 0.75 0.77 0.79 0.76 0.64 0.77 0.82 0.77 0.81 0.79 0.83 0.79 0.79 1.37 1.26 1.23 1.28 1.21 1.21 1.33 1.57 1.39

10842513 10827665 10731138 10859627 10904356 10827448 10779792 10938173 10730021 10933128 10870890 10903058 10939164 10861356 10765728 10905970 10774341 10766994 10717798 10707376 10801535 10822348 10853149 10723687 10859772

similar to RIKEN cDNA 2010011I20




BC079459

31


E2F transcription factor 5 gonadotropin inducible ovarian transcription factor 1 inhibitor of DNA binding 3 polymerase (RNA) III (DNA directed) polypeptide K zinc finger, CCHC domain containing 11

-----------------------------------

29 30 33 39 42 50 50 54 70 103 103 108 122 140 142 350 754

1.30 1.20 1.21 1.31 1.21 1.20 1.20 1.67 1.21 1.58 1.58 1.24 1.44 1.21 1.66 1.39 1.34

10805577 10736417 10884738 10792132 10768369 10795260 10940007 10922266 10741664 10791602 10833416 10930569 10809882 10805722 10939699 10820008 10930602

List 12. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat CA1 of the Hippocampus as Compared to Non-Stressed F3-Vinclozolin ('Str-Vin vs Nst-Vin' contrast), 379 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis Bace2 NM_001002802 -35 0.71 10750513 beta-site APP-cleaving enzyme 2 Dap3 NM_001011950 -83 0.81 10824373 death associated protein 3 TRAF-interacting protein with forkheadTifab NM_001025029 -14 0.82 10793961 associated domain, family member B tumor necrosis factor (ligand) superfamily, member 4 Tnfsf4 NM_053552 -22 0.80 10765092 ENSRNOT000000388 tumor necrosis factor, alpha-induced protein 8Tnfaip8l3 30 -18 0.70 10917501 like 3 Cell Cycle Cenpc1 NM_001004098 -73 0.79 10772107 centromere protein C 1 Cep70 NM_001017470 -56 0.78 10912464 centrosomal protein 70kDa ENSRNOT000000303 centrosome and spindle pole associated protein Cspp1 45 -128 0.71 10875091 1 minichromosome maintenance complex Mcm8 NM_001106514 -17 0.80 10840112 component 8 Prc1 NM_001107529 -29 0.73 10708214 protein regulator of cytokinesis 1 CytoskeletonECM Cdh8 NM_053393 -335 0.61 10805767 cadherin 8 carcinoembryonic antigen-related cell adhesion Ceacam10 NM_173339 9.6 1.30 10705034 molecule 10 Crtac1 NM_134401 -121 0.73 10715431 cartilage acidic protein 1 Dynlrb2 NM_001108451 -42 0.62 10811283 dynein light chain roadblock-type 2 Gjb6 NM_053388 -134 0.79 10784120 gap junction protein, beta 6 Fank1 NM_001008347 -14 0.78 10711777 fibronectin type 3 and ankyrin repeat domains 1 Hapln1 NM_019189 -92 0.81 10812399 hyaluronan and proteoglycan link protein 1 Krt17 NM_212545 8 1.22 10747296 keratin 17 killer cell lectin-like receptor, subfamily A, Klra5 NM_198746 -13 0.78 10866236 member 5 LOC290704 ENSRNOT000000596 14 1.28 10787918 similar to palladin




32


Marveld2 Mosc1 Myom2 RGD1563615 Tbca Ttll3 Ttll4 Development Cecr6 Crygb Gsc2 Gtl3 Lce1l Lhx2 Meox1 Myocd Ntn1 Nlgn1 Popdc2 Ptov1 Robo3 Tecpr1 Vgll3 Rcan3 Syt17 Sntg1 Tert Vasn DNA Repair Rad52 Electron Transport Cox18 Etfb LOC10017491 0 Prdx6 Pdcl Pdcl2 LOC691211

73 NM_001108936

-15

0.72

10820965

NM_001100811 NM_001169141 ENSRNOT000000465 25 NM_001013245 NM_001108640 ENSRNOT000000230 67

-9 -11

0.83 0.80

10770503 10792621

53 -51 -20

1.24 0.78 0.81

10793444 10899579 10857767

MARVEL domain containing 2 MOCO sulphurase C-terminal domain containing 1 myomesin 2 similar to Contactin associated protein-like 3 precursor (Cell recognition molecule Caspr3) tubulin folding cofactor A tubulin tyrosine ligase-like family, member 3

-45

0.81

10924392

tubulin tyrosine ligase-like family, member 4

XM_001058567 NM_001109875 NM_001108846 NM_001037978 NM_001109493 NM_001106571 NM_001108837 NM_182667 AY028417 NM_053868 NM_199113 NM_001008304 NM_001108135 NM_001037191 ENSRNOT000000423 16 NM_001012746 NM_138849 ENSRNOT000000096 79 NM_053423 NM_001109382

20 -9.9 17 -113 -48 -87 23 22 56 -156 -22 -95 -21 -81

1.25 0.80 1.24 0.78 0.76 0.78 1.20 1.26 1.52 0.73 0.83 0.80 0.75 0.82

10865198 10928555 10752382 10805895 10824769 10835958 10747682 10743652 10743781 10822545 10754179 10721504 10916201 10756638

cat eye syndrome chromosome region, candidate 6 homolog (human) crystallin, gamma B goosecoid homeobox 2 gene trap locus 3 late cornified envelope 1L LIM homeobox 2 mesenchyme homeobox 1 myocardin netrin 1 neuroligin 1 popeye domain containing 2 prostate tumor overexpressed 1 roundabout homolog 3 (Drosophila) tectonin beta-propeller repeat containing 1

-44 37 193

0.71 1.37 1.25

10749839 10880610 10725235

vestigial like 3 (Drosophila) RCAN family member 3 synaptotagmin XVII

-100 -22 41

0.77 0.80 1.21

10867345 10717517 10740701

syntrophin, gamma 1 telomerase reverse transcriptase vasorin

NM_001106617

-46

0.80

10858260

RAD52 homolog (S. cerevisiae)

NM_001106000 NM_001004220

-95 -110

0.81 0.67

10771819 10706339

COX18 cytochrome c oxidase assembly homolog (S. cerevisiae) electron-transfer-flavoprotein, beta polypeptide

NM_001131003 NM_053576 NM_022247 ENSRNOT000000029 53 ENSRNOT000000508 23

-129 -362 -115

0.71 0.66 0.83

10804552 10769218 10844776

glutaredoxin-like protein peroxiredoxin 6 phosducin-like

-12

0.74

10772243

phosducin-like 2

-9.9

0.79

10724991

similar to Cytochrome c, somatic

Epigenetics




33


DPH5 homolog (S. cerevisiae) HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae) histone deacetylase 8 T-box 20

Dph5

NM_001017449

-32

0.82

10818581

Hfm1 Hdac8 Tbx20 Growth Factors Angpt1 Dner Gdf10 Il15 Kng1l1 Rxfp1 Tgfb2

XM_002724927 NM_001126373 NM_001108132

-17 -65 12

0.80 0.78 1.20

10771099 10938734 10915817

NM_053546 BC086329 NM_024375 NM_013129 NM_001009628 NM_201417 NM_031131

-30 -186 -30 -19 -63 133 212

0.69 0.80 0.72 0.78 0.66 1.80 1.62

10903529 10929482 10786905 10806899 10755135 10823819 10770577

Wnt7a Immune Response Cd244 Cd302 Cd5l Igh-1a Il22 LOC688858 RT1-M6-1 RT1-M6-2 Spag8 Metabolism & Transport Aadacl2 Abhd3 Acsbg1 Adh1 Adsl Apof Ass1

NM_001100473

-48

0.75

10864094

angiopoietin 1 delta growth differentiation factor 10 interleukin 15 kininogen 1-like 1 relaxin transforming growth factor, beta 2 wingless-type MMTV integration site family, member 7A

NM_022259 NM_001013916 NM_001025685 BC088254 ENSRNOT00000009776 XM_001068599 NM_001008852 NM_001008853 NM_001173555

-13 -35 -31 -12 -15 -224 -49 -36 -14

0.77 0.82 0.77 0.81 0.82 0.78 0.72 0.71 0.83

10765625 10845508 10816270 10892533 10895618 10759581 10827686 10827691 10876426

Cd244 molecule, natural killer cell receptor 2B4 CD302 molecule Cd5 molecule-like immunoglobulin heavy chain 1a (serum IgG2a) interleukin 22 similar to CD209a antigen RT1 class I, locus M6, gene 1 RT1 class I, locus M6, gene 2 sperm associated antigen 8

ENSRNOT00000067870 NM_001106162 NM_134389 NM_019286 NM_001130503 NM_001024351 NM_013157

-8 -276 -230 27 -63 -16 27

0.82 0.80 0.81 1.27 0.83 0.80 1.37

10815616 10803207 10917568 10819379 10897854 10893064 10835355

Atp5o

NM_138883

-101

0.83

10753198

Cad Coq9 Crot

NM_001105710 NM_001035257 NM_031987

-20 -60 -58

0.82 0.81 0.80

10888872 10809251 10860548

Gcsh Gk Gstm5 Gstm7 Hsd11b1

NM_133598 NM_024381 NM_172038 NM_031154 NM_017080

-127 -79 -245 -296 -226

0.80 0.77 0.81 0.78 0.67

10811293 10938219 10818291 10825890 10770795

Kcnq5l Peci Pgcp Phyh Ppcdc Ppid Prodh

ENSRNOT00000040034 NM_001006966 NM_031640 NM_053674 NM_001108763 NM_001004279 NM_001135778

-337 -75 -53 -136 -16 -399 -134

0.57 0.80 0.80 0.81 0.83 0.75 0.70

10926975 10794769 10896028 10799558 10917754 10816008 10752352

arylacetamide deacetylase-like 2 abhydrolase domain containing 3 acyl-CoA synthetase bubblegum family member 1 alcohol dehydrogenase 1 (class I) adenylosuccinate lyase apolipoprotein F argininosuccinate synthetase 1 ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase coenzyme Q9 homolog (S. cerevisiae) carnitine O-octanoyltransferase glycine cleavage system protein H (aminomethyl carrier) glycerol kinase glutathione S-transferase, mu 5 glutathione S-transferase, mu 7 hydroxysteroid 11-beta dehydrogenase 1 potassium voltage-gated channel, subfamily Q, member 5-like peroxisomal D3,D2-enoyl-CoA isomerase plasma glutamate carboxypeptidase phytanoyl-CoA 2-hydroxylase phosphopantothenoylcysteine decarboxylase peptidylprolyl isomerase D (cyclophilin D) proline dehydrogenase




34


Pygb Sephs2 Slc14a1

NM_013188 NM_001079889 NM_019346

-296 50 -166

0.78 1.20 0.80

10840700 10725993 10805335

Slc16a3 Slc45a2

NM_030834 NM_001107653

39 -9

1.26 0.82

10740209 10813686

Timm17a

NM_019351

-152

0.80

10890170

Timm8a1 Tst Ugt2b Urod Proteolysis

NM_053370 NM_012808 NM_031533 NM_019209

-119 -82 -9 -83

0.81 0.83 0.80 0.79

10939289 10905284 10771951 10878926

Herpud1 Htra1 Kdelc1 Klk15 LOC360228 Osgep Prep Prss23 Rnf146 Timp4 Ubc

NM_053523 NM_031721 NM_001108217 ENSRNOT00000038353 NM_001003706 NM_001100510 NM_031324 NM_001007691 NM_001012060 NM_001109393 NM_017314

-74 -397 -57 -27 -33 -22 -64 -34 -165 -70 350

0.80 0.74 0.83 0.75 0.75 0.79 0.78 0.82 0.80 0.81 1.34

10809328 10711566 10923000 10706498 10736875 10783147 10830654 10708541 10702424 10864732 10758134

Ubr7 Usp3 Receptors & Binding Proteins Adora2b Adra1d Bdkrb1 Efcab2 Efcab6 Fgfr3

NM_001007705 NM_001025424

-74 -20

0.82 0.81

10886494 10918345

NM_017161 NM_024483 NM_030851 NM_001105977 ENSRNOT00000015447 NM_053429

-36 -81 -17 -24 16 -64

0.76 0.75 0.83 0.70 1.34 0.79

10734291 10850087 10886644 10766065 10905871 10777748

Gabrg1 Gfral Ifngr2 Igfbp5 Iscu MGC112715 Mt2A Mt2A Olr1069 Olr1088 Olr120 Olr1321 Olr1418 Olr1557 Olr1640 Olr1714 Olr1734 Olr221

NM_080586 ENSRNOT00000052341 NM_001108313 NM_012817 NM_001105936 NM_001044300 NM_001137564 NM_001137564 NM_001000522 ENSRNOT00000012907 NM_001000154 NM_001000792 NM_001000008 NM_001000050 NM_001000099 NM_214456 NM_001001119 NM_001000200

-432 -9.8 -129 212 -121 59 -626 -346 -12 25 -21 10.4 -12 -10.1 -12 -56 -9 24

0.65 0.82 0.76 1.70 0.83 1.22 0.67 0.61 0.78 1.22 0.75 1.22 0.79 0.75 0.82 0.81 0.74 1.41

10772544 10918752 10750211 10928837 10762887 10829993 10809399 10827989 10900095 10900905 10724297 10909287 10742927 10753565 10783355 10830818 10827639 10724609




35


phosphorylase, glycogen; brain selenophosphate synthetase 2 solute carrier family 14 (urea transporter), member 1 solute carrier family 16, member 3 (monocarboxylic acid transporter 4) solute carrier family 45, member 2 translocase of inner mitochondrial membrane 17 homolog A (yeast) translocase of inner mitochondrial membrane 8 homolog a1 (yeast) thiosulfate sulfurtransferase UDP glycosyltransferase 2 family, polypeptide B uroporphyrinogen decarboxylase homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 HtrA serine peptidase 1 KDEL (Lys-Asp-Glu-Leu) containing 1 kallikrein-related peptidase 15 WDNM1 homolog O-sialoglycoprotein endopeptidase prolyl endopeptidase protease, serine, 23 ring finger protein 146 tissue inhibitor of metalloproteinase 4 ubiquitin C ubiquitin protein ligase E3 component n-recognin 7 (putative) ubiquitin specific peptidase 3

adenosine A2B receptor adrenergic, alpha-1D-, receptor bradykinin receptor B1 EF-hand calcium binding domain 2 EF-hand calcium binding domain 6 fibroblast growth factor receptor 3 gamma-aminobutyric acid (GABA) A receptor, gamma 1 GDNF family receptor alpha like interferon gamma receptor 2 insulin-like growth factor binding protein 5 iron-sulfur cluster scaffold homolog (E. coli) platelet receptor Gi24 metallothionein 2A metallothionein 2A olfactory receptor 1069 olfactory receptor 1088 olfactory receptor 120 olfactory receptor 1321 olfactory receptor 1418 olfactory receptor 1557 olfactory receptor 1640 olfactory receptor 1714 olfactory receptor 1734 olfactory receptor 221

Olr423 Olr495 Olr560 Olr582 Olr584 Olr629 Olr689 Olr734 Olr809 Olr828 Olr996 Ptbp2 Sec14l2 Tlr2 Trhr V1rd23 V1rg6 Vom2r66 Signaling Anxa6 Arhgap1 Aurkb

NM_001000391 NM_001000310 NM_001000325 NM_001000662 NM_001000661 NM_001001058 NM_001000997 NM_001000617 NM_001000849 NM_001000991 NM_001000700 NM_001005555 NM_053801 NM_198769 NM_013047 NM_001008947 NM_001008957 ENSRNOT00000051621

12 11 -13 -42 -20 -29 45 -28 17 35 33 -290 -98 10.0 -23 -16 -14 74

1.25 1.28 0.83 0.63 0.76 0.72 1.31 0.78 1.25 1.30 1.42 0.80 0.82 1.25 0.72 0.83 0.78 1.37

10835879 10846974 10837518 10837545 10847074 10847109 10847176 10847242 10855092 10858150 10893375 10826418 10778043 10823970 10896394 10718780 10894297 10774903

olfactory receptor 423 olfactory receptor 495 olfactory receptor 560 olfactory receptor 582 olfactory receptor 584 olfactory receptor 629 olfactory receptor 689 olfactory receptor 734 olfactory receptor 809 olfactory receptor 828 olfactory receptor 996 polypyrimidine tract binding protein 2 SEC14-like 2 (S. cerevisiae) toll-like receptor 2 thyrotropin releasing hormone receptor vomeronasal 1 receptor, D23 vomeronasal 1 receptor, G6 vomeronasal 2 receptor, 66

NM_024156 NM_001107747 NM_053749

-464 127 -12

0.50 1.28 0.77

10742712 10837960 10734853

Dbi Dusp4 Efna1 Gbp4 Gm2a Gpr139

NM_031853 NM_022199 NM_053599 ENSRNOT00000022648 NM_172335 NM_001024241

-92 -51 23 -18 -99 17

0.78 0.75 1.25 0.76 0.82 1.24

10931154 10792035 10824439 10819512 10733690 10725286

Grin2c Ick Igtp Inpp5j LOC304239 Map6d1

NM_012575 NM_138886 NM_001008765 NM_133562 ENSRNOT00000049215 NM_001108844

-57 92 -10.1 -84 -66 77

0.81 1.39 0.82 0.75 0.63 1.23

10748891 10911780 10733790 10777958 10756334 10752200

MGC109340 Ndrg3 Nek6 Pdk2

NM_001024267 NM_001013923 NM_182953 NM_030872

-167 277 -64 -161

0.77 1.22 0.75 0.82

10935036 10851210 10835964 10746469

Pkib

NM_001076553

-13

0.82

10830216

Plekho2 Pygm

ENSRNOT00000042633 NM_012638

-48 -95

0.68 0.77

10918288 10713382

RGD1562165 Rilpl2 Rit1

ENSRNOT00000029187 NM_001004205 NM_001109185

-11 -24 -89

0.82 0.81 0.82

10876836 10758212 10816607

Sgef Sh3bp4

ENSRNOT00000019553 NM_022693

-73 128

0.73 1.50

10815663 10925264

Slamf1 Socs4 Srp14

NM_001109078 NM_001107256 NM_001106497

16 -37 -125

1.23 0.83 0.81

10765639 10779668 10848434

annexin A6 Rho GTPase activating protein 1 aurora kinase B diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein) dual specificity phosphatase 4 ephrin A1 guanylate binding protein 4 GM2 ganglioside activator G protein-coupled receptor 139 glutamate receptor, ionotropic, N-methyl Daspartate 2C intestinal cell kinase interferon gamma induced GTPase inositol polyphosphate-5-phosphatase J similar to RalA binding protein 1 MAP6 domain containing 1 similar to Microsomal signal peptidase 23 kDa subunit (SPase 22 kDa subunit) (SPC22 N-myc downstream regulated gene 3 NIMA (never in mitosis gene a)-related kinase 6 pyruvate dehydrogenase kinase, isozyme 2 protein kinase (cAMP-dependent, catalytic) inhibitor beta pleckstrin homology domain containing, family O member 2 phosphorylase, glycogen, muscle similar to GABA(A) receptor-associated protein like 2 Rab interacting lysosomal protein-like 2 Ras-like without CAAX 1 Src homology 3 domain-containing guanine nucleotide exchange factor SH3-domain binding protein 4 signaling lymphocytic activation molecule family member 1 suppressor of cytokine signaling 4 signal recognition particle 14




36


Transcription Ankdd1a Ankrd60 Ccdc129 Ccdc148 Ccdc153 Ccdc30 Ccdc37 Ccdc46

ENSRNOT00000033512 ENSRNOT00000055082 ENSRNOT00000045930 NM_001107732 NM_001013953 ENSRNOT00000011325 ENSRNOT00000024222 NM_001105849

-19 -16 -19 -28 -72 -41 -21 -22

0.73 0.82 0.72 0.78 0.56 0.81 0.69 0.76

10918281 10852149 10855741 10845443 10909463 10871570 10864025 10739277

Clip4 Creb3l3 E2f5 Elk1 Foxj2 Gtf2ird1 Haus1 Hint1 Kbtbd11 Klhl36 Luzp1 March3

NM_001013942 NM_001012115 ENSRNOT00000014361 NM_001108059 NM_001109352 NM_001001504 NM_138864 ENSRNOT00000006471 NM_001107326 NM_001017511 AF181259 NM_001007759

-117 18 -25 78 42 -18 36 -20 -43 -19 -20 -40

0.69 1.22 0.72 1.24 1.23 0.80 1.25 0.70 0.74 0.81 0.80 0.73

10888620 10893630 10718609 10936520 10858529 10757829 10805313 10862836 10792660 10808356 10873012 10804541

Noc4l Nop58 Nutf2 Ovca2 Pnrc1

NM_001014129 NM_021754 NM_001007629 NM_001109036 NM_173322

-40 -117 -117 -74 237

0.81 0.82 0.80 0.81 1.20

10759342 10923670 10807386 10744904 10875863

Polr3k Ppara RGD1565987 RGD1565987 Ssx1

NM_001014259 NM_013196 ENSRNOT00000048737 ENSRNOT00000048737 ENSRNOT00000030146

-204 -16 -47 -46 -9

0.77 0.79 0.79 0.80 0.82

10843132 10898359 10877694 10756806 10936947

Tada2b Zcchc3 Zcchc6 Zfp212 Znf488 Translation & Protein Modification

NM_001170455 ENSRNOT00000009859 ENSRNOT00000067726 ENSRNOT00000009054 ENSRNOT00000031496

-54 17 136 -76 15

0.77 1.21 1.36 0.80 1.30

10773358 10850793 10793708 10855203 10790433

Cwc22 Eif4e3 LOC500148

ENSRNOT00000037684 NM_001106612 NM_001035253

-66 -159 57

0.75 0.62 1.29

10846661 10864425 10862792

Lsm3 Mrps16

NM_001106611 NM_001109518

-134 -69

0.80 0.81

10857310 10779159

Qtrtd1 Rbm45 RGD1560186 RGD1561736 RGD1563551 RGD1565117

ENSRNOT00000000317 NM_153306 ENSRNOT00000049634 XM_001061583 ENSRNOT00000047507 ENSRNOT00000045687

-30 -65 -9 -80 -9 9

0.81 0.81 0.78 0.76 0.75 1.22

10751196 10837056 10766758 10940411 10865372 10895828




37


ankyrin repeat and death domain containing 1A ankyrin repeat domain 60 coiled-coil domain containing 129 coiled-coil domain containing 148 coiled-coil domain containing 153 coiled-coil domain containing 30 coiled-coil domain containing 37 coiled-coil domain containing 46 CAP-GLY domain containing linker protein family, member 4 cAMP responsive element binding protein 3-like 3 E2F transcription factor 5 ELK1, member of ETS oncogene family forkhead box J2 GTF2I repeat domain containing 1 HAUS augmin-like complex, subunit 1 histidine triad nucleotide binding protein 1 kelch repeat and BTB (POZ) domain containing 11 kelch-like 36 (Drosophila) leucine zipper protein 1 membrane-associated ring finger (C3HC4) 3 nucleolar complex associated 4 homolog (S. cerevisiae) nucleolar protein NOP58 nuclear transport factor 2 candidate tumor suppressor in ovarian cancer 2 proline-rich nuclear receptor coactivator 1 polymerase (RNA) III (DNA directed) polypeptide K peroxisome proliferator activated receptor alpha similar to F-box and leucine-rich repeat protein 18 similar to F-box and leucine-rich repeat protein 18 synovial sarcoma, X breakpoint 1 transcriptional adaptor 2 (ADA2 homolog, yeast)beta zinc finger, CCHC domain containing 3 zinc finger, CCHC domain containing 6 Zinc finger protein 212 zinc finger protein 488

CWC22 spliceosome-associated protein homolog (S. cerevisiae) eukaryotic translation initiation factor 4E member 3 similar to 40S ribosomal protein S7 (S8) LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) mitochondrial ribosomal protein S16 queuine tRNA-ribosyltransferase domain containing 1 RNA binding motif protein 45 similar to ribosomal protein L37 similar to ribosomal protein L10 similar to ribosomal protein L31 similar to 40S ribosomal protein S26

Rnase4 Rpl28 Rplp2 Miscellaneous & Unknown Btbd16 Dtwd1 Dydc2 Fam123c Fam158a Fam198b

NM_020082 NM_022697 NM_001030021

-87 -186 366

0.78 0.81 1.24

10779832 10718863 10776809

ribonuclease, RNase A family 4 ribosomal protein L28 ribosomal protein, large P2

NM_001017464 NM_001013921 NM_001134797 ENSRNOT00000033700 BC086432 NM_199105

-11 33 12 -24 -54 32

0.82 1.23 1.20 0.73 0.83 1.29

10711532 10839438 10790647 10922449 10783799 10816017

BTB (POZ) domain containing 16 DTW domain containing 1 DPY30 domain containing 2 family with sequence similarity 123C family with sequence similarity 158, member A family with sequence similarity 198, member B

LOC100359838

XM_002728978

14

1.23

10833596

ret finger protein-like 4-like

LOC100364350 LOC362863 LOC363306 LOC502684 LOC679307 LOC687395 Lsmd1 Luc7l3 MGC94282 Mterfd2 Ptcd3 RGD1305089 RGD1310641 RGD1559961 RGD1563072 RGD1565059 Rtn4ip1 Tlcd1 Tmem186 Tmem208

XM_002725175 NM_001170605 ENSRNOT00000043269 NM_001025060 ENSRNOT00000038733 ENSRNOT00000006406 NM_001105794 NM_001108291 NR_027366 NM_001037209 NM_001134718 NM_001106730 NM_001079701 NM_001163736 NM_001107981 NM_001127562 NM_001107644 NM_001013858 NM_001025756 NM_001106179

-69 -14 86 -17 -12 -139 -149 -202 23 -32 -105 -80 -14 -71 73 -18 -72 -91 -38 -64

0.79 0.82 1.27 0.68 0.73 0.82 0.80 0.76 1.32 0.78 0.80 0.81 0.78 0.80 1.31 0.83 0.76 0.76 0.83 0.82

10790658 10894643 10921328 10840826 10774245 10838278 10734970 10746286 10865838 10929991 10863158 10884648 10875910 10745785 10872059 10823456 10830630 10745214 10731596 10807211

Tmtc2 Tsku ttc21a Wdr60 Yjefn3 EST's RGD1311575 LOC499565 LOC689296 RGD1306462 RGD1305457 LOC497940 RGD1565158 RGD1306446

XM_001080732 NM_001009965 ENSRNOT00000043831 ENSRNOT00000006144 ENSRNOT00000065345

-77 -32 -22 -40 -26

0.78 0.82 0.68 0.82 0.78

10902080 10723822 10914271 10892677 10787684

NACHT and WD repeat domain containing 1-like first gene upstream of Nt5dc3 hypothetical protein LOC363306 hypothetical protein LOC502684 hypothetical protein LOC679307 similar to CG9240-PA LSM domain containing 1 LUC7-like 3 (S. cerevisiae) similar to 5930416I19Rik protein MTERF domain containing 2 Pentatricopeptide repeat domain 3 similar to 1110008L16Rik protein similar to hypothetical protein similar to novel protein similar to hypothetical protein FLJ38984 similar to hypothetical protein E130311K13 reticulon 4 interacting protein 1 TLC domain containing 1 transmembrane protein 186 transmembrane protein 208 transmembrane and tetratricopeptide repeat containing 2 tsukushin tetratricopeptide repeat domain 21A WD repeat domain 60 YjeF N-terminal domain containing 3

ENSRNOT00000002908 NM_001047946 NM_001109531 BC097453 NM_001009430 BC079326 ENSRNOT00000061709 NM_001008554 ---------------

-46 -12 -14 -13 15 -9 -36 -10.3 -702 -270 -170 -92 -91 -68 -65

0.75 0.81 0.80 0.83 1.25 0.77 0.71 0.81 0.76 0.83 0.75 0.71 0.74 0.60 0.61

10776361 10814179 10890190 10906065 10894842 10744306 10740325 10772030 10886848 10865696 10932269 10894227 10906590 10914877 10807957




38


hypothetical LOC289568 LRRGT00038 similar to expressed sequence C79407 similar to RIKEN cDNA 1700019P01 similar to RIKEN cDNA 1700023M03 similar to RIKEN cDNA 2810408A11 similar to RIKEN cDNA 4921537P18 similar to RIKEN cDNA 9930032O22 gene

-----------------------------------------------------------------------------------------------------------------




-63 -63 -61 -53 -52 -49 -47 -47 -46 -45 -44 -42 -40 -39 -38 -36 -33 -33 -31 -30 -27 -25 -24 -22 -22 -22 -21 -20 -19 -19 -18 -17 -17 -17 -16 -16 -13 -13 -13 -12 -12 -12 -11 -11 -11 -11 -11 -11 -10.5 -10.4 -10.3 -10.2 -9.5 -9 -9 -9

0.79 0.78 0.76 0.77 0.75 0.83 0.80 0.64 0.78 0.74 0.48 0.79 0.69 0.77 0.64 0.65 0.77 0.78 0.83 0.81 0.83 0.81 0.54 0.80 0.77 0.60 0.74 0.77 0.81 0.76 0.75 0.81 0.82 0.70 0.72 0.81 0.83 0.83 0.83 0.75 0.80 0.76 0.81 0.79 0.77 0.80 0.82 0.82 0.77 0.80 0.83 0.75 0.74 0.82 0.81 0.78

10783318 10721694 10758724 10729852 10749975 10869187 10914901 10782509 10738221 10804712 10776289 10878965 10726483 10897004 10802574 10840477 10717953 10796438 10812493 10798486 10938820 10736814 10800599 10701814 10755550 10807883 10818656 10729554 10706224 10781888 10764047 10705392 10840180 10701666 10708304 10876998 10717011 10719289 10841596 10803721 10894874 10908152 10719036 10763316 10839972 10788343 10860416 10827409 10890166 10830185 10910545 10776737 10752253 10862921 10876750 10863051

39


-------------------------------------------------------------------

-9 -9 -8 -8 -7 -7 9 9 11 14 14 16 18 21 21 24 25 27 28 29 33 34 42 51 53 64 68 70 111 149 161 176 195

0.78 0.78 0.79 0.80 0.82 0.82 1.23 1.22 1.26 1.21 1.35 1.44 1.23 1.36 1.50 1.25 1.32 1.21 1.30 1.33 1.29 1.43 1.33 1.38 1.28 1.37 1.59 1.23 1.29 1.23 1.28 1.54 1.24

10729120 10934683 10905970 10791547 10708451 10703566 10788345 10874046 10894850 10868595 10935227 10886244 10742118 10816498 10774341 10801535 10777433 10764400 10823676 10731606 10930576 10838077 10896201 10863026 10880526 10797939 10722816 10833808 10925808 10833287 10813246 10741664 10867364

List 13. Genes Expressed Differentially in Non-Stressed F3-Vinclozolin Rat CA3 of the Hippocampus as Compared to Non-Stressed F3-Control ('Nst-Vin vs Nst-Con' contrast), 64 genes and EST's Mean _diff

Ratio

Affymetrix ID

Gene Title

NM_001013125

80

1.20

10731229

bifunctional apoptosis regulator

Pno1

NM_199083

117

1.24

10778568

partner of NOB1 homolog (S. cerevisiae)

LOC689303

ENSRNOT00000041918

-13

0.75

10797584

similar to vitamin A-deficient testicular protein 11like

Gene Symbol

GenBank_Reference Sequence

Apoptosis Bfar Development

Growth Factors Kng1

NM_012696

8

1.20

10751988

kininogen 1

Prl8a7

NM_022537

-11

0.83

10795057

prolactin family 8, subfamily a, member 7




40


Immune Response

XM_002729360

23

1.27

10863000

similar to [Human Ig rearranged gamma chain mRNA, V_J_C region and complete cds.], gene product

Acaa2

NM_130433

-70

0.79

10802691

acetyl-Coenzyme A acyltransferase 2

Chi3l4

XM_001069770

-17

0.82

10825768

chitinase 3-like 4

Kcnf1

NM_001169104

-62

0.81

10889326

potassium voltage-gated channel, subfamily F, member 1

Pop5

NM_001105752

60

1.31

10762717

processing of precursor 5, ribonuclease P

RGD1560402

XM_574850

-57

0.81

10812969

similar to Phosphoglycerate kinase 1

Ugt2b34

ENSRNOT00000002728

11

1.23

10771993

UDP glucuronosyltransferase 2 family, polypeptide B34

Serpinb3

NM_001008887

-9

0.82

10766988

serine protease inhibitor B3

Ube2n

NM_053928

200

1.20

10860546

ubiquitin-conjugating enzyme E2N

Olr1545

NM_001001105

-26

0.73

10750630

olfactory receptor 1545

Epha5

NM_001169137

221

1.20

10772128

Eph receptor A5

Fgfr1

NM_024146

153

1.23

10792304

Fibroblast growth factor receptor 1

Wbp2

NM_138975

155

1.21

10749108

WW domain binding protein 2

LOC365559

ENSRNOT00000035259

-19

0.82

10832838

similar to mannose-6-phosphate receptor binding protein 1

Wipf3

NM_147211

102

1.21

10855637

WAS

Rcn3

NM_001008694

25

1.21

10721641

reticulocalbin 3, EF-hand calcium binding domain

Sipa1l3

ENSRNOT00000038929

159

1.25

10720504

signal-induced proliferation-associated 1 like 3

Tbc1d25

NM_001106955

50

1.23

10932416

TBC1 domain family, member 25

RGD1560691

NM_001107365

204

1.23

10796307

similar to calcium/calmodulin-dependent protein kinase 1D

LOC502812 Metabolism & Transport

Proteolysis

Receptors & Binding Proteins

Signaling

Transcription




41


Nrip3 Miscellaneous & Unknown Fam50a LOC502894 LOC678714 RGD1563774 Tmem60 EST's RGD1566265 RGD1306282

EST's RGD1566265 RGD1306282




NM_001108498

412

1.21

10724785

nuclear receptor interacting protein 3

NM_001170573 NM_001025064 ENSRNOT00000051350 ENSRNOT00000045483 ENSRNOT00000018040

-40 90 -74 -12 90

0.81 1.24 0.80 0.80 1.24

10940358 10884921 10862027 10875576 10860269

family with sequence similarity 50, member A hypothetical protein LOC502894 hypothetical protein LOC678714 similar to hypothetical protein 4930474N05 transmembrane protein 60

NM_001134589 ENSRNOT00000038294 BC090072 ---------------------------------------------------------------

97 13 -30 -241 -130 -117 -83 -70 -60 -58 -57 -56 -46 -39 -34 -33 -30 -30 -30 -30 -28 -25 -23 -21 -20 -16 -16 -16 -12 20 20 24 52 70

1.22 1.26 0.64 0.80 0.77 0.74 0.58 0.74 0.74 0.61 0.63 0.81 0.81 0.73 0.69 0.74 0.64 0.64 0.64 0.64 0.76 0.77 0.72 0.83 0.79 0.82 0.79 0.83 0.82 1.35 1.42 1.23 1.21 1.39

10939002 10902621 10759435 10813353 10794749 10838153 10939888 10908655 10878386 10859195 10928205 10860184 10857448 10778586 10902762 10933576 10756268 10756270 10756272 10759445 10703289 10789042 10714409 10722413 10909129 10936019 10861395 10800386 10885297 10920741 10888777 10714177 10852671 10937568

similar to RIKEN cDNA 2610002M06 similar to RIKEN cDNA 4432406C05

NM_001134589 ENSRNOT00000038294 BC090072 -----------------

97 13 -30 -241 -130 -117 -83 -70 -60 -58 -57

1.22 1.26 0.64 0.80 0.77 0.74 0.58 0.74 0.74 0.61 0.63

10939002 10902621 10759435 10813353 10794749 10838153 10939888 10908655 10878386 10859195 10928205

similar to RIKEN cDNA 2610002M06 similar to RIKEN cDNA 4432406C05

42


-----------------------------------------------

-56 -46 -39 -34 -33 -30 -30 -30 -30 -28 -25 -23 -21 -20 -16 -16 -16 -12 20 20 24 52 70

0.81 0.81 0.73 0.69 0.74 0.64 0.64 0.64 0.64 0.76 0.77 0.72 0.83 0.79 0.82 0.79 0.83 0.82 1.35 1.42 1.23 1.21 1.39

10860184 10857448 10778586 10902762 10933576 10756268 10756270 10756272 10759445 10703289 10789042 10714409 10722413 10909129 10936019 10861395 10800386 10885297 10920741 10888777 10714177 10852671 10937568

List 14. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat CA3 of the Hippocampus as Compared to Stressed F3-Control ('St-Vin vs St-Con' contrast), 23 genes and EST's Gene Symbol Cell Cycle Cspp1 Immune Response Cd38 Receptors & Binding Proteins Olr1443 Olr1567 Olr666 Olr921 Signaling Rab25 Transcription Zbtb41 Translation & Protein Modification RGD1565170 Miscellaneous & Unknown Fam75a4 RGD1563482 EST's




GenBank_Reference Sequence

Mean _diff

Ratio

Affymetrix ID

ENSRNOT00000008480

-105

0.83

10875093

centrosome and spindle pole associated protein 1

NM_013127

-30

0.82

10777232

CD38 molecule

NM_001000018 NM_001000043 NM_001000924 NM_001001385

25 16 13 44

1.22 1.23 1.21 1.29

10733884 10752235 10847144 10900010

olfactory receptor 1443 olfactory receptor 1567 olfactory receptor 666 olfactory receptor 921

NM_001107687

17

1.20

10824339

RAB25, member RAS oncogene family

ENSRNOT00000015596

-153

0.82

10764404

zinc finger and BTB domain containing 41

ENSRNOT00000043836

20

1.32

10780763

similar to 60S ribosomal protein L23a

BC085936 NM_001109065

-13 -25

0.77 0.82

10796941 10761736

family with sequence similarity 75, member A4 similar to hypothetical protein FLJ38663

-------

-419 -275 -227

0.80 0.81 0.81

10886870 10886890 10886988

43


Gene Title

-----------

-140 -92 -22 -15 12

0.82 0.82 0.80 0.82 1.24

10908810 10870979 10938245 10892616 10759473

---

18

1.21

10724999

---

21

1.35

10703461

---

59

1.39

10726672

---

392

1.33

10902859

List 15. Genes Expressed Differentially in Stressed F3-Control Rat CA3 of the Hippocampus as Compared to Non-Stressed F3-Control ('Str-Con vs Nst-Con' contrast), 50 genes and EST's Gene Symbol Cell Cycle Cdk2ap2 CytoskeletonECM Lce1c Spock3 Growth Factors Kng1 Immune Response LOC287167 Metabolism & Transport Acaa2

GenBank_Reference Sequence

Mean _diff

Ratio

Affymetrix ID

NM_001109498

-38

0.83

10712786

CDK2-associated protein 2

ENSRNOT00000012420 NM_001107310

-6 -227

0.82 0.80

10824752 10791346

late cornified envelope 1C sparc

NM_012696

10.5

1.27

10751988

kininogen 1

NM_001013853

-85

0.82

10741765

globin, alpha

NM_130433

-60

0.82

10802691

Gene Title

Atp6ap1l Hbb MGC72973 Hba-a2 Hbb Proteolysis Rnf135 Receptors & Binding Proteins Olr1222 Olr582 Olr654 Snupn Signaling Ctnnal1 Sfn Transcription

ENSRNOT00000044237 NM_033234 NM_198776 NM_013096 NM_033234

-52 -374 -324 -1192 -311

0.77 0.63 0.63 0.70 0.72

10820308 10724311 10724319 10741756 10724315

acetyl-Coenzyme A acyltransferase 2 ATPase, H+ transporting, lysosomal accessory protein 1-like hemoglobin, beta beta-glo hemoglobin alpha, adult chain 2 hemoglobin, beta

ENSRNOT00000005428

8

1.22

10736636

ring finger protein 135

NM_001000440 NM_001000662 NM_001000636 NM_001004270

12 24 41 -74

1.20 1.25 1.28 0.82

10909147 10837545 10847125 10910252

olfactory receptor 1222 olfactory receptor 582 olfactory receptor 654 snurportin 1

NM_001106649 XM_001065560

-90 50

0.81 1.20

10876896 10872572

catenin (cadherin associated protein), alpha-like 1 stratifin

Lrrcc1

NM_001100645

98

1.21

10822290

LOC500210 Yeats2

XM_002726403 NM_001109057

9.8 -61

1.22 0.81

10863370 10755501




44


leucine rich repeat and coiled-coil domain containing 1 similar to High mobility group protein 1 (HMG-1) (High mobility group protein B1) (Amphoterin) (Heparin-binding protein p30) YEATS domain containing 2

Miscellaneous & Unknown Fam102b RGD1562660 RGD1563774 EST's LOC100365935

NM_001163568 ENSRNOT00000044160 ENSRNOT00000045483

-94 -59 -11

0.83 0.76 0.83

10826137 10809906 10875576

family with sequence similarity 102, member B RGD1562660 similar to hypothetical protein 4930474N05

BC160895 ---------------------------------------------------

59 -78 -70 -66 -47 -35 -32 -29 -27 -20 -16 -15 -12 10.3 13 16 18 19 23 25 25 51 57 65 72 75

1.20 0.66 0.81 0.71 0.67 0.71 0.83 0.74 0.81 0.82 0.80 0.79 0.82 1.24 1.27 1.24 1.23 1.24 1.31 1.27 1.21 1.22 1.22 1.20 1.26 1.47

10833346 10726672 10798900 10878386 10778586 10722413 10843159 10703289 10844062 10881476 10861395 10744141 10857000 10857203 10742245 10894848 10791329 10894798 10717136 10877933 10898117 10867699 10940126 10774605 10923212 10866205

rCG22129-like

List 16. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat CA3 of the Hippocampus as Compared to NonStressed F3-Vinclozolin ('Str-Vin vs Nst-Vin' contrast), 202 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis Snn NM_001034083 -162 0.81 10740408 stannin Cell Cycle Ccnk NM_001109672 -50 0.83 10886714 cyclin K Cnnm1 NM_001107593 -111 0.83 10730272 cyclin M1 Cspp1 ENSRNOT00000008480 -120 0.83 10875087 centrosome and spindle pole associated protein 1 RGD1563620 ENSRNOT00000033132 -146 0.82 10815924 similar to retinoblastoma binding protein 4 CytoskeletonECM Cadm2 NM_001047102 -330 0.80 10752679 cell adhesion molecule 2 Elmo2 NM_001134955 -168 0.82 10851753 engulfment and cell motility 2 Fxc1 NM_053371 9 1.27 10833834 fractured callus expressed transcript 1 Jph1 NM_001106630 -105 0.77 10867081 junctophilin 1 Krtap14l ENSRNOT00000064058 52 1.51 10752948 keratin associated protein 14 like Lum NM_031050 15 1.21 10895083 lumican Mast3 NM_001134796 -121 0.81 10787447 microtubule associated serine Mfap3 NM_001007609 -68 0.83 10733726 microfibrillar-associated protein 3 microtubule associated monoxygenase, calponin and Mical2 NM_001139508 -184 0.80 10709951 LIM domain containing 2




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Pcdh1 Development Clmn Bbx Shisa6 Dpy19l3 Lrrc8b Msl1

ENSRNOT00000026324

-197

0.83

10804117

protocadherin 1

NM_001106755 NM_001079938 ENSRNOT00000057509 NM_001135835 NM_001107204 NM_001107048

-177 -72 -200 -196 -106 -126

0.78 0.82 0.77 0.83 0.79 0.82

10892035 10750900 10743715 10721126 10775278 10738071

Nedd4l Odz3 Sez6

NM_001008300 NM_001169133 ENSRNOT00000048543

-192 -91 -234

0.83 0.78 0.82

10802231 10788086 10736119

Sema3e Skil

NM_001106579 ENSRNOT00000013191

-180 -169

0.81 0.79

10860457 10822637

LOC689303 Syn3 Sncg Wasf1 Epigenetics Hist1h2bc Hist1h2bn Mir483 Brd2 Prmt8 Golgi Apparatus

ENSRNOT00000041918 NM_017109 NM_031688 NM_001025114

11 -23 47 -374

1.27 0.83 1.20 0.80

10797584 10894465 10790471 10833952

calmin bobby sox homolog (Drosophila) shisa homolog 6 (Xenopus laevis) dpy-19-like 3 (C. elegans) leucine rich repeat containing 8 family, member B male-specific lethal 1 homolog (Drosophila) neural precursor cell expressed, developmentally down-regulated 4-like odz, odd Oz seizure related 6 homolog (mouse) sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E SKI-like oncogene similar to vitamin A-deficient testicular protein 11like synapsin III synuclein, gamma (breast cancer-specific protein 1) WAS protein family, member 1

NM_001109400 NM_001106114 NR_032112 NM_212495 ENSRNOT00000006878

-90 -51 173 -100 -184

0.81 0.82 1.31 0.82 0.83

10798488 10798494 10727006 10828364 10865790

histone cluster 1, H2bc histone cluster 1, H2bn microRNA mir-483 bromodomain containing 2 protein arginine methyltransferase 8

Gga3 Immune Response Nfat5

NM_001108304

-106

0.82

10748973

golgi associated, gamma adaptin ear containing, ARF binding protein 3

NM_001107425

-119

0.80

10807638

LOC685767 Metabolism & Transport Aldh1a2 Aox4 Bco2 Cacnb4

ENSRNOT00000048964

20

1.22

10751086

NM_053896 ENSRNOT00000033068 NM_001127712 NM_001105733

34 -208 38 -114

1.31 0.80 1.21 0.83

10911380 10923476 10917215 10845306

Cacng8 Commd10

NM_080696 NM_001004276

-172 -155

0.82 0.83

10718561 10801584

Cyp4a2

NM_001044770

42

1.27

10878780

Elovl6 Hs6st2

NM_134383 ENSRNOT00000040165

-111 -84

0.83 0.74

10819005 10939725

Ift88

NM_001107266

-54

0.82

10780765

Kcnd2 Kcnn2 Nup205 Plcb1 Scn3b

NM_031730 NM_019314 NM_001108620 NM_001077641 NM_139097

-291 -177 -45 -196 -487

0.82 0.81 0.83 0.83 0.83

10853905 10801520 10854494 10840142 10909328




46


nuclear factor of activated T-cells 5 similar to OX-2 membrane glycoprotein precursor (MRC OX-2 antigen) (CD200 antigen)

aldehyde dehydrogenase 1 family, member A2 aldehyde oxidase 4 beta-carotene oxygenase 2 calcium channel, voltage-dependent, beta 4 subunit calcium channel, voltage-dependent, gamma subunit 8 COMM domain containing 10 cytochrome P450, family 4, subfamily a, polypeptide 2 ELOVL family member 6, elongation of long chain fatty acids (yeast) heparan sulfate 6-O-sulfotransferase 2 intraflagellar transport 88 homolog (Chlamydomonas) potassium voltage-gated channel, Shal-related subfamily, member 2 potassium intermediate nucleoporin 205 phospholipase C, beta 1 (phosphoinositide-specific) sodium channel, voltage-gated, type III, beta

St8sia3

NM_013029

-234

0.83

10802222

Trpc5 Trak2 Proteolysis Adam23 Dpp6

NM_080898 NM_133560

-222 -207

0.72 0.81

10932726 10928307

NM_001029899 NM_022850

-143 -258

0.82 0.81

10923877 10859886

Hecw2 Receptors & Binding Proteins Baiap2 Cttnbp2 Epha5 Lphn3 Lrp6 Olr105 Olr1143 Olr1226 Olr1364 Olr1400 Olr1567 Olr1637 Olr1714 Olr1726 Olr546 Olr566 Olr712 Olr886 Olr921 RGD1566059

NM_001108218

-113

0.83

10928001

NM_057196 NM_001114401 NM_001169137 NM_130822 NM_001107892 NM_001000146 NM_001001017 NM_001000442 NM_001000858 NM_001001096 NM_001000043 NM_001000503 NM_214456 NM_001000896 NM_001001054 NM_001000665 NM_001000624 NM_001001382 NM_001001385 ENSRNOT00000046220

-190 -245 -226 -184 -96 91 56 48 139 23 17 52 83 102 73 26 9 17 46 54

0.83 0.83 0.83 0.82 0.82 1.21 1.20 1.27 1.23 1.20 1.25 1.22 1.32 1.34 1.30 1.22 1.27 1.23 1.31 1.28

10740094 10861171 10772128 10776264 10866374 10724274 10908171 10909154 10740780 10733098 10752235 10783186 10830818 10830830 10847049 10837528 10847215 10899979 10900010 10838423

Sorl1 V1rc1 Vom2r24 Vom2r56 Signaling Csrnp3 Defb49 Defa24 Dixdc1 Dgki Dclk2 Frmd4b Jak1 Ksr1

NM_053519 NM_001008906 NM_001099493 NM_001099484

-227 24 32 13

0.83 1.22 1.27 1.26

10916493 10855806 10703632 10901190

ENSRNOT00000007197 NM_001037527 NM_001013053 NM_001037654 NM_198782 NM_001009691 ENSRNOT00000010717 NM_053466 NM_001108284

-120 55 16 -72 -129 -179 -51 -219 -72

0.81 1.21 1.21 0.79 0.80 0.79 0.81 0.83 0.82

10836490 10926837 10792538 10917260 10861843 10824091 10864371 10878286 10745303

Ppp1r9a Rab11fip2 Sipa1l3 Sh3bp4 Snx19 Snx32 Tbc1d25 Transcription

NM_053473 NM_001107447 ENSRNOT00000038929 NM_022693 NM_001108131 ENSRNOT00000036745 NM_001106955

-149 -128 -187 -55 -129 -56 -49

0.83 0.83 0.76 0.82 0.79 0.81 0.82

10853614 10731140 10720504 10925264 10908764 10727884 10932416




47


ST8 alpha-N-acetyl-neuraminide alpha-2,8sialyltransferase 3 transient receptor potential cation channel, subfamily C, member 5 trafficking protein, kinesin binding 2 ADAM metallopeptidase domain 23 dipeptidylpeptidase 6 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2

BAI1-associated protein 2 cortactin binding protein 2 EphA5 latrophilin 3 low density lipoprotein receptor-related protein 6 olfactory receptor 105 olfactory receptor 1143 olfactory receptor 1226 olfactory receptor 1364 olfactory receptor 1400 olfactory receptor 1567 olfactory receptor 1637 olfactory receptor 1714 olfactory receptor 1726 olfactory receptor 546 olfactory receptor 566 olfactory receptor 712 olfactory receptor 886 olfactory receptor 921 similar to olfactory receptor Olfr1289 sortilin-related receptor, LDLR class A repeatscontaining vomeronasal 1 receptor, C1 vomeronasal 2 receptor, 24 vomeronasal 2 receptor, 56 cysteine-serine-rich nuclear protein 3 defensin beta 49 defensin, alpha, 24 DIX domain containing 1 diacylglycerol kinase, iota doublecortin-like kinase 2 FERM domain containing 4B Janus kinase 1 kinase suppressor of ras 1 protein phosphatase 1, regulatory (inhibitor) subunit 9A RAB11 family interacting protein 2 (class I) signal-induced proliferation-associated 1 like 3 SH3-domain binding protein 4 sorting nexin 19 sorting nexin 32 TBC1 domain family, member 25

Ankrd45 Ahctf1 Bcl6 Cnot7 Dnajb5 E2f5 Ing2 Med14 Myt1l Mef2d

ENSRNOT00000003857 ENSRNOT00000035875 NM_001107084 NM_001107313 NM_001108004 ENSRNOT00000014361 NM_001106083 ENSRNOT00000066480 NM_053888 NM_030860

-161 -131 -80 -196 -114 -39 -63 -177 -157 -91

0.82 0.80 0.80 0.82 0.83 0.65 0.82 0.83 0.83 0.81

10765051 10770261 10751931 10788414 10868428 10718609 10788134 10932279 10884001 10816470

Pcif1 Tdpoz1 Tcf3 Yeats2 Zbtb45 Zeb2 Zfp354b Zfp462 Znf667 Dhx57 Translation & Protein Modification Eif1b Eif4g3

NM_001108605 XM_345239 NM_001107865 NM_001109057 NM_001107478 NM_001033701 ENSRNOT00000004902 ENSRNOT00000047225 NM_001008557 ENSRNOT00000037705

-54 45 59 -59 -26 -317 -14 -121 -62 -66

0.82 1.21 1.21 0.82 0.82 0.81 0.83 0.71 0.83 0.82

10842221 10824790 10863277 10755501 10704281 10845072 10742466 10869158 10718696 10887990

NM_001106867 NM_001106693

-197 -133

0.82 0.83

10914349 10873226

Imp3

NM_001108152

-171

0.83

10910249

Prpf38b RGD1559743 RGD1559955 Miscellaneous & Unknown Fam102b LOC681205 LOC685340 Prb1 RGD1562660 RGD1563065 RGD1308297 RGD1564195 RGD1306556 RGD1564200 RGD1560883 Trim2 EST's LOC290577 RGD1564814 RGD1305664

NM_001024305 XM_001077121 ENSRNOT00000046179

-86 22 72

0.83 1.21 1.35

10826130 10920785 10925757

eukaryotic translation initiation factor 1B eukaryotic translation initiation factor 4 gamma, 3 IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) PRP38 pre-mRNA processing factor 38 (yeast) domain containing B similar to 40S ribosomal protein S16 similar to 40S ribosomal protein S17

NM_001163568 ENSRNOT00000020640 ENSRNOT00000039568 L17318 ENSRNOT00000044160 ENSRNOT00000002978 BC082039 ENSRNOT00000049044 ENSRNOT00000000901 NM_001108969 ENSRNOT00000018479 NM_001108552

-109 15 10 241 -34 -105 -166 -79 -35 -104 -50 -344

0.81 1.23 1.23 1.24 0.83 0.76 0.82 0.82 0.80 0.81 0.83 0.83

10826137 10921453 10933970 10866332 10809906 10772788 10785745 10725914 10759227 10867587 10812297 10824017

family with sequence similarity 102, member B hypothetical protein LOC681205 hypothetical protein LOC685340 proline-rich protein BstNI subfamily 1 RGD1562660 similar to 3110047P20Rik protein similar to CG10084-PA similar to hypothetical protein similar to hypothetical protein A530094D01 similar to hypothetical protein MGC34646 similar to KIAA0825 protein tripartite motif-containing 2

XM_002725158 ENSRNOT00000038133 ENSRNOT00000004829 -------------

40 28 -102 -103 -88 -77 -73 -72 -72

1.33 1.25 0.81 0.78 0.83 0.81 0.82 0.83 0.83

10786993 10775737 10743626 10722718 10867008 10743702 10869817 10801258 10924669

hypothetical LOC290577 similar to CDNA sequence BC061212 similar to KIAA0672 gene product




48


ankyrin repeat domain 45 AT hook containing transcription factor 1 B-cell CLL CCR4-NOT transcription complex, subunit 7 DnaJ (Hsp40) homolog, subfamily B, member 5 E2F transcription factor 5 inhibitor of growth family, member 2 mediator complex subunit 14 myelin transcription factor 1-like myocyte enhancer factor 2D PDX1 C-terminal inhibiting factor 1 TD and POZ domain containing 1 transcription factor 3 YEATS domain containing 2 zinc finger and BTB domain containing 45 zinc finger E-box binding homeobox 2 zinc finger protein 354B zinc finger protein 462 zinc finger protein 667 DEAH (Asp-Glu-Ala-Asp

-----------------------------------------------------------------------------------------------------------------




-71 -52 -52 -48 -48 -46 -29 -28 -23 -21 -18 -17 -13 -10 7 9 10 11 11 12 14 14 15 15 17 17 18 21 22 26 26 26 28 28 33 33 40 41 41 42 46 47 52 53 55 55 68 69 125 128 211 246 346 415 685 733

0.81 0.81 0.81 0.78 0.82 0.80 0.79 0.59 0.82 0.77 0.81 0.83 0.81 0.78 1.24 1.30 1.23 1.29 1.21 1.24 1.27 1.31 1.26 1.24 1.21 1.22 1.21 1.25 1.23 1.34 1.77 1.22 1.30 1.53 1.23 1.36 1.24 1.23 1.21 1.27 1.26 1.20 1.30 1.30 1.25 1.24 1.76 1.27 1.25 1.25 1.26 1.37 1.24 1.35 1.39 1.52

10869614 10743680 10743699 10765036 10758033 10765038 10761268 10888777 10714177 10815350 10749977 10882888 10857000 10887693 10933227 10850313 10794940 10788028 10796768 10806925 10908156 10892794 10886267 10822733 10718428 10787820 10884694 10789042 10934042 10828152 10850319 10769619 10877933 10703461 10927211 10933576 10715188 10904230 10901836 10797939 10800328 10717353 10704169 10773461 10934978 10913627 10859195 10802272 10892656 10934792 10737708 10719159 10909581 10902859 10788070 10815996

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