The FASEB Journal article fj.10-172452. Published online October 18, 2010.
The FASEB Journal • Review
ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS Eric Pasmant,*,†,1 Audrey Sabbagh,*,† Michel Vidaud,*,† and Ivan Bie`che*,† *Unite´ Mixte de Recherche (UMR)745 Institut National de la Sante´ et de la Recherche Me´dicale (INSERM), Universite´ Paris Descartes, Faculte´ des Sciences Pharmaceutiques et Biologiques, Paris, France; and †Service de Biochimie et Ge´ne´tique Mole´culaire, Hoˆpital Beaujon, Clichy, France ABSTRACT A large noncoding RNA called ANRIL (for antisense noncoding RNA in the INK4 locus) has been identified within the p15/CDKN2B-p16/CDKN2Ap14/ARF gene cluster. While the exact role of ANRIL awaited further elucidation, common disease genomewide association studies (GWAS) have surprisingly identified the ANRIL gene as a genetic susceptibility locus shared associated by coronary disease, intracranial aneurysm and also type 2 diabetes. Expression studies have confirmed the coregulation of p15/CDKN2B, p16/ CDKN2A, p14/ARF, and ANRIL. Among the cluster, ANRIL expression showed the strongest association with the multiple phenotypes linked to the 9p21.3 region. More recent GWAS also identified ANRIL as a risk locus for gliomas and basal cell carcinomas in accordance with the princeps observation. Moreover, a mouse model has confirmed the pivotal role of ANRIL in regulation of CDKN2A/B expression through a cisacting mechanism and its implication in proliferation and senescence. The implication of ANRIL in cellular aging has provided an attractive unifying hypothesis to explain its association with various susceptibility risk factors. ANRIL identification emphasizes the underestimated role of long noncoding RNAs. Many GWAS have identified trait-associated SNPs that felt in noncoding genomic regions. It is conceivable to anticipate that long, noncoding RNAs will map to many of these “gene deserts.”—Pasmant, E., Sabbagh, A., Vidaud, M., Bie`che, I. ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J. 25, 000 – 000 (2011). www.fasebj.org
Key Words: long ncRNA 䡠 susceptibility locus 䡠 p15/CDKN2Bp16/CDKN2A-p14/ARF gene cluster Hereditary cutaneous malignant melanoma (CMM) is a well-established syndrome (1). One of the main CMM loci has been mapped to chromosome arm 9p21. Three candidate tumor suppressor genes have been identified in this region: p15/CDKN2B (cyclin-dependent kinase inhibitor 2B; alias INK4B for inhibitor of cyclin-dependent kinase 4B) encodes p15 protein, p16/CDKN2A (alias INK4A) encodes p16 protein, and p14/ARF (alternate reading frame) encodes p14ARF protein. p14ARF protein is encoded by an alternative exon 1 (1) and by exons 2 and 3 of the p16/CDKN2A gene in a different reading 0892-6638/10/0025-0001 © FASEB
frame. Consequently, p16 and p14ARF share no homology at the amino acid level and have significantly different functions. p15 and p16 are specific cyclin-dependent kinase (CDK) 4/CDK6 inhibitors in the retinoblastoma (Rb) pathway, and inactivation of p15 and/or p16 allows cells to escape cell cycle arrest in G1. p14ARF acts in both the p53 and Rb pathways by interacting with MDM2, a protein common to the two pathways. p14ARF binds MDM2 and promotes its degradation, resulting in p53 activation and G1 and G2 arrest. p16/CDKN2A is currently the most clinically relevant melanoma susceptibility gene in 9p21. By contrast, germ-line mutations in p14/ARF are rare and have not been described in p15/CDKN2B. Joint predisposition to neural system tumors (NSTs) and to CMM has been described in a few families, segregating as a mendelian disorder. This hereditary syndrome has been termed the melanoma-astrocytoma syndrome (OMIM 155755) owing to the presence of astrocytomas in the first family to be characterized (2). We have previously detected a large germ-line deletion (403 kb; chr9:21,926,315–22,329,545; numbered in February 2009 human reference sequence GRCh37/ hg19) which included the entire p15/CDKN2B-p16/ CDKN2A-p14/ARF gene cluster, in the largest CMMNST syndrome family known to date, suggesting a contiguous gene syndrome (3). The additional germline deletion of p15/CDKN2B and p14/ARF could have explained the NST predisposition. However, in this study, we also identified a new long noncoding RNA (ncRNA) that we called ANRIL (for antisense noncoding RNA in the INK4 locus; OMIM 613149) within the germ-line deletion. The ANRIL gene (NR_003529; also called CDKN2BAS) contains 19 exons, spans a region of 126.3 kb, and is transcribed in a 3834-bp mRNA in the antisense orientation of the p15/CDKN2B-p16/CDKN2Ap14/ARF gene cluster. ANRIL intron 1 overlaps the two
1 Correspondence: UMR745 INSERM, Universite´ Paris Descartes, Faculte´ des Sciences Pharmaceutiques et Biologiques, 4 avenue de l’Observatoire, 75006, Paris, France. E-mail:
[email protected] doi: 10.1096/fj.10-172452
1
exons of p15/CDKN2B (Fig. 1A). The 5⬘ end of the first exon of the ANRIL gene is located ⬃300 bp upstream of the transcription start site of the p14/ARF gene. Moreover, expression of ANRIL mainly coclustered with p14/ ARF both in physiological (various normal human tissues) and in pathological conditions (various human tumors), suggesting that these two genes may share a coordinated transcription (3). Recently, new insights into ANRIL and p14/ARF transcription coregulation have been gained since CTCF-binding sites have been mapped in the CpG island overlapping the ANRIL-p14/ARF promoters (4). CTCF (CCCTC-binding factor) is a major zinc-finger protein with insulator and chromatin barrier activity critical for transcription of the p15/CDKN2B-p16/CDKN2Ap14/ARF locus.
RECENT RESULTS While the exact role of ANRIL awaited further elucidation, common disease genomewide association studies (GWAS) have surprisingly identified the ANRIL gene as a genetic susceptibility locus associated with coronary disease, intracranial aneurysm (5– 8), and also type 2 diabetes (9, 10). The association between ANRIL and these diseases has been since confirmed by expression studies (11–13). Indeed, genotypes of common singlenucleotide polymorphisms (SNPs) in ANRIL linked to increased risk of atherosclerotic diseases have been associated with decreased expression of ANRIL transcripts in purified peripheral blood T cells (11). Expression studies have confirmed the coregulation of the
Figure 1. Genomic organization of the p15/CDKN2B-p16/CDKN2A-p14/ ARF-ANRIL gene cluster at 9p21.3 locus. A) Boxes, location of exons (approximately to scale). Exons 1␣, 1␣2, and 1␣3 of p16/CDKN2A encode p16 protein, whereas exon 1, spliced to exons 2 and 3 of p16/CDKN2A in a different reading frame and transcribed using a different promoter, encodes p14ARF protein. The ANRIL gene overlaps the two exons of p15/ CDKN2B and is transcribed in the orientation opposite to the p15/ CDKN2B-p16/CDKN2A-p14/ARF gene cluster. Exon 1 of ANRIL is present ⬃300 bp upstream of the transcription start site of p14/ARF (exon 1). B) Location of 20 SNPs selected from GWAS and linkage disequilibrium (LD) blocks on 9p21.3. Physical positions of 20 SNPs are illustrated on the basis of the National Center for Biotechnology Information database (February 2009; human reference sequence GRCh37/ hg19). Distinct groups are associated with glioma (red arrows; rs1063192, rs2157719, rs1412829, and rs4977756), basal cell carcinoma (purple arrow; rs2151280), nasopharyngeal carcinoma (black arrow; rs1412829), breast cancer (blue arrow; rs1011970), coronary disease (numerous neighboring SNPs showing strong LD in ANRIL 3⬘ region and indicated by orange arrows), intracranial aneurysm (gray arrow; rs1333040), and type 2 diabetes (green arrow; rs10811661). SNP data of the European HapMap sample (CEU) have been used to look at LD patterns. LD blocks are shown by r2 measures. The r2 values (⫻100) for the marker pairs are listed in the corresponding boxes. High pairwise LD between markers is illustrated with dark shading. SNP rs10811661 associated with type 2 diabetes is totally independent from the other SNPs of the locus (r2⬍1%). ⌬58 corresponds to the genomic interval in ANRIL 3⬘ end (58 kb: ANRIL exons 13 to 19) orthologous to the deleted interval in the transgenic mouse generated by Visel et al. (26). 2
Vol. 25
February 2010
The FASEB Journal 䡠 www.fasebj.org
PASMANT ET AL.
transcription of p15/CDKN2B, p16/CDKN2A, p14/ARF, and ANRIL but have also shown the transcript complexity of the locus. The ANRIL gene was found to have ⱖ8 transcript variants with tissue-specific expression (12). It is worth noting that ANRIL expression showed the strongest association with the multiple phenotypes linked to the 9p21.3 region, as compared to the three other genes of the cluster (14, 15). Moreover, a conserved sequence in ANRIL (designated CNS3), which included the artery disease susceptibility SNP rs1333045, was demonstrated to have an enhancer activity in a reporter gene experiment in primary aortic sooth muscle cells (13). These observations suggested that modulation of ANRIL expression mediates susceptibility to several important human diseases. Despite these advances, the pathophysiology underlying the link between ANRIL and coronary heart disease remained not understood. More recently, additional GWAS identified ANRIL as a risk locus for several cancers including breast cancer, nasopharyngeal carcinoma, basal cell carcinoma, and glioma (Fig. 1B) (16 –19). ANRIL thus appeared to be an unexpected major target of GWAS for various diseases (http://www.genome.gov/gwastudies/). Moreover, the identification of ANRIL as a glioma susceptibility locus was in accordance with the princeps identification of a germ-line deletion of ANRIL in a family with a hereditary predisposition to melanoma with neural system tumors (3). A study has suggested that susceptibility to the various diseases identified by GWAS could be conferred by distinct, tightly linked SNPs in the ANRIL locus (Fig. 1B) (20). These SNPs may alter expression of one of the numerous ANRIL spliced transcripts, which, in turn, might affect cellular proliferation pathways (13). However, a putative explanation underlying the association between ANRIL and miscellaneous unrelated diseases has emerged from a study concerning the decline in the replicative function of the stem cell with advancing age (21). Indeed, mechanisms that suppress the development of cancer, such as senescence and apoptosis, which rely on telomere shortening and the activities of p53 and p15/ CDKN2B-p16/CDKN2A-p14/ARF-ANRIL locus, may also induce an unwanted consequence: a decline in the replicative function of certain stem cell types with advancing age. Sharpless and DePinho (21) have suggested that this altered regenerative capacity contributed to some aspects of human age-associated conditions, such as cancers, atherosclerosis, and type 2 diabetes. The decline in the regenerative capacity of the insulin-producing  cell of the pancreatic islet was observed in type 2 diabetes development (22), and cell proliferation is an important event in both atherosclerosis and aneurysm formation (13). Thus, the implication of ANRIL in cellular aging via the regulation of the p15/CDKN2B-p16/CDKN2A-p14/ARF locus, has provided an attractive unifying hypothesis to explain its association with various susceptibility risk factors. ANRIL, A LONG NCRNA HOTSPOT IN GWAS
PROSPECTS AND PREDICTIONS In this regard, very recent studies have gained new insights in mechanisms by which ANRIL may regulate expression of the protein-coding genes at the p15/ CDKN2B-p16/CDKN2A-p14/ARF locus via a polycombmediated epigenetic silencing (23–26). Yap et al. (23) have suggested that ANRIL participates directly in epigenetic transcriptional repression of the locus. Chromobox 7 (CBX7) within the polycomb repressive complex 1 (PRC1) has been shown to bind to ANRIL. In concert with recognition of methylation of histone H3 at lysine 27 (H3K27me3), binding to ANRIL contributes to CBX7 function and affects the ability of CBX7 to repress the locus and control senescence (23). Moreover, MOV10, a putative RNA helicase previously implicated in post-transcriptional gene silencing by associating with chromatin in a long ncRNA-dependent manner, have been shown to copurify and interact with CBX7 (24). Small hairpin RNA (shRNA)-mediated knockdown of MOV10 resulted in up-regulation of CDKN2A at both the RNA and protein levels, accompanied by displacement of CBX7 components and H3K27me3, from the promoter region and first exon of CDKN2A (24). Taken together, the results of these two studies (23, 24) suggest a major role for a long ncRNA (very probably ANRIL) in transcriptional repression of the p15/CDKN2B-p16/CDKN2A-p14/ARF locus by polycombs group (PcG) proteins. Additional epigenetic modifiers, such as the histone demethylases JMJD3 and JHDM1B, the SWI/SNF chromatin remodeling complex, and DNA methyltransferases, could regulate this locus, interplaying with PRCs (25). Otherwise, Visel et al. (26) have generated a recombinant mouse strain harboring a 70-kb deletion on chromosome 4qC4/5. This region is orthologous to the human 58-kb noncoding interval on 9p21.3, including the 3⬘ end of ANRIL (⌬58: exons 13 to 19), and conferring an increased risk of coronary disease (Fig. 1B). The Chr4⌬70kb/⌬70kb mice were viable but showed increased mortality both during development and as adults. Primary cultures of Chr4⌬70kb/⌬70kb aortic smooth muscle cells exhibited excessive proliferation and diminished senescence, a cellular phenotype consistent with accelerated coronary disease pathogenesis. Cardiac expression of Cdkn2a and Cdkn2b was severely reduced in the transgenic mice, confirming that the noncoding risk interval has a pivotal role in regulation of Cdkn2a/b expression through a cis-acting mechanism (26). Further in vitro studies (cultured cells) and in vivo studies (animal models) will be required for full confirmation of the role of ANRIL in the locus regulation and in the various physiopathological processes highlighted by GWAS. Although the current literature is dominated by short RNAs (microRNAs), ANRIL identification emphasizes the underestimated role of long ncRNAs that, rather than encoding protein, act functionally at the RNA level (27, 28). Although we currently lack satisfactory classifications for these long ncRNAs, their transcripts are arbitrarily considered to be longer than ⬃200 nucleotides. Around 3500 human long ncRNAs 3
have been identified to date. Large-scale sequencing of full-length cDNA libraries will progressively build a more detailed repertoire of ncRNAs and will aid in the prediction of their widespread functionalities, complemented by experimental analyses of individual examples to determine the mechanisms by which long ncRNAs act. Moreover, it is worth noting that many GWAS have identified trait-associated SNPs that fell in noncoding genomic regions (29, 30). It is conceivable to anticipate that long noncoding RNAs will map to many of these “gene deserts.”
REFERENCES 1. 2. 3.
4.
5.
6.
7.
8.
4
10.
Hayward, N. K. (2003) Genetics of melanoma predisposition. Oncogene 22, 3053–3062 Kaufman, D. K., Kimmel, D. W., Parisi, J. E., and Michels, V. V. (1993) A familial syndrome with cutaneous malignant melanoma and cerebral astrocytoma. Neurology 43, 1728 –1731 Pasmant, E., Laurendeau, I., He´ron, D., Vidaud, M., Vidaud, D., and Bie`che, I. (2007) Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family, identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res. 67, 3963–3969 Rodriguez, C., Borgel, J., Court, F., Cathala, G., Forne´, T., and Piette, J. (2010) CTCF is a DNA methylation-sensitive positive regulator of the INK/ARF locus. Biochem. Biophys. Res. Commun. 392, 129 –134 McPherson, R., Pertsemlidis, A., Kavaslar, N., Stewart, A., Roberts, R., Cox, D. R., Hinds, D. A., Pennacchio, L. A., TybjaergHansen, A., Folsom, A. R., Boerwinkle, E., Hobbs, H. H., and Cohen, J. C. (2007) A common allele on chromosome 9 associated with coronary heart disease. Science 316, 1488 –1491 Helgadottir, A., Thorleifsson, G., Magnusson, K.P., Gre´tarsdottir, S., Steinthorsdottir, V., Manolescu, A., Jones, G. T., Rinkel, G. J., Blankensteijn, J. D., Ronkainen, A., Ja¨a¨skela¨inen, J. E., Kyo, Y., Lenk, G. M., Sakalihasan, N., Kostulas, K., Gottsa¨ter, A., Flex, A., Stefansson, H., Hansen, T., Andersen, G., Weinsheimer, S., Borch-Johnsen, K., Jorgensen, T., Shah, S.H., Quyyumi, A.A., Granger, C. B., Reilly, M. P., Austin, H., Levey, A. I., Vaccarino, V., Palsdottir, E., Walters, G. B., Jonsdottir, T., Snorradottir, S., Magnusdottir, D., Gudmundsson, G., Ferrell, R. E., Sveinbjornsdottir, S., Hernesniemi, J., Niemela¨, M., Limet, R., Andersen, K., Sigurdsson, G., Benediktsson, R., Verhoeven, E. L., Teijink, J.A., Grobbee, D. E., Rader, D. J., Collier, D. A., Pedersen, O., Pola, R., Hillert, J., Lindblad, B., Valdimarsson, E. M., Magnadottir, H. B., Wijmenga, C., Tromp, G., Baas, A. F., Ruigrok, Y. M., van Rij, A. M., Kuivaniemi, H., Powell, J. T., Matthiasson, S. E., Gulcher, J. R., Thorgeirsson, G., Kong, A., Thorsteinsdottir, U., and Stefansson, K. (2008) The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm. Nat. Genet. 40, 217–224 Bilguvar, K., Yasuno, K., Niemela¨, M., Ruigrok, Y. M., von Und Zu Fraunberg, M., van Duijn, C. M., van den Berg, L. H., Mane, S., Mason, C. E., Choi, M., Gaa´l, E., Bayri, Y., Kolb, L., Arlier, Z., Ravuri, S., Ronkainen, A., Tajima, A., Laakso, A., Hata, A., Kasuya, H., Koivisto, T., Rinne, J., Ohman, J., Breteler, M. M., Wijmenga, C., State, M. W., Rinkel, G. J., Hernesniemi, J., Ja¨a¨skela¨inen, J. E., Palotie, A., Inoue, I., Lifton, R. P., and Gu¨nel, M. (2008) Susceptibility loci for intracranial aneurysm in European and Japanese populations. Nat. Genet. 40, 1472–1477 Yasuno, K., Bilguvar, K., Bijlenga, P., Low, S. K., Krischek, B., Auburger, G., Simon, M., Krex, D., Arlier, Z., Nayak, N., Ruigrok, Y. M., Niemela¨, M., Tajima, A., von und zu Fraunberg, M., Do´czi, T., Wirjatijasa, F., Hata, A., Blasco, J., Oszvald, A., Kasuya, H., Zilani, G., Schoch, B., Singh, P., Stu¨er, C., Risselada, R., Beck, J., Sola, T., Ricciardi, F., Aromaa, A., Illig, T., Schreiber, S., van Duijn, C. M., van den Berg, L. H., Perret, C., Proust, C., Roder, C., Ozturk, A. K., Gaa´l, E., Berg, D., Geisen, C.,
Vol. 25
February 2010
9.
11.
12.
13.
14.
15.
16.
17.
Friedrich, C. M., Summers, P., Frangi, A. F., State, M. W., Wichmann, H. E., Breteler, M. M., Wijmenga, C., Mane, S., Peltonen, L., Elio, V., Sturkenboom, M. C., Lawford, P., Byrne, J., Macho, J., Sandalcioglu, E. I., Meyer, B., Raabe, A., Steinmetz, H., Ru¨fenacht, D., Ja¨a¨skela¨inen, J. E., Hernesniemi, J., Rinkel, G. J., Zembutsu, H., Inoue, I., Palotie, A., Cambien, F., Nakamura, Y., Lifton, R. P., and Gu¨nel, M. (2010) Genome-wide association study of intracranial aneurysm identifies three new risk loci. Nat. Genet. 42, 420 – 425 Zeggini, E., Weedon, M. N., Lindgren, C. M., Frayling, T. M., Elliott, K. S., Lango, H., Timpson, N. J., Perry, J. R., Rayner, N. W., Freathy, R. M., Barrett, J. C., Shields, B., Morris, A. P., Ellard, S., Groves, C. J., Harries, L. W., Marchini, J. L., Owen, K. R., Knight, B., Cardon, L. R., Walker, M., Hitman, G. A., Morris, A. D., Doney, A. S., Wellcome Trust Case Control Consortium (WTCCC), McCarthy, M. I., and Hattersley, A. T. (2007) Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 316, 1336 – 1341 Scott, L. J., Mohlke, K. L., Bonnycastle, L. L., Willer, C. J., Li, Y., Duren, W. L., Erdos, M. R., Stringham, H. M., Chines, P. S., Jackson, A. U., Prokunina-Olsson, L., Ding, C. J., Swift, A. J., Narisu, N., Hu, T., Pruim, R., Xiao, R., Li, X. Y., Conneely, K. N., Riebow, N. L., Sprau, A. G., Tong, M., White, P. P., Hetrick, K. N., Barnhart, M. W., Bark, C. W., Goldstein, J. L., Watkins, L., Xiang, F., Saramies, J., Buchanan, T. A., Watanabe, R. M., Valle, T. T., Kinnunen, L., Abecasis, G. R., Pugh, E. W., Doheny, K. F., Bergman, R. N., Tuomilehto, J., Collins, F. S., and Boehnke, M. (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316, 1341–1345 Liu, Y., Sanoff, H. K., Cho, H., Burd, C. E., Torrice, C., Mohlke, K. L., Ibrahim, J. G., Thomas, N. E., and Sharpless, N. E. (2009) INK4/ARF transcript expression is associated with chromosome 9p21 variants linked to atherosclerosis. PLoS One 4, e5027 Folkersen, L., Kyriakou, T., Goel, A., Peden, J., Ma¨larstig, A., Paulsson-Berne, G., Hamsten, A., Hugh Watkins, Franco-Cereceda, A., Gabrielsen, A., Gabrielsen, A, and Eriksson, P.; Procardis Consortium. (2009) Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. PLoS One 4, e7677 Jarinova, O., Stewart, A. F., Roberts, R., Wells, G., Lau, P., Naing, T., Buerki, C., McLean, B. W., Cook, R. C., Parker, J. S., and McPherson, R. (2009) Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus. Arterioscler. Thromb. Vasc. Biol. 29, 1671–1677 Holdt, L. M., Beutner, F., Scholz, M., Gielen, S., Ga¨bel, G., Bergert, H., Schuler, G., Thiery, J., and Teupser, D. (2010) ANRIL expression is associated with atherosclerosis risk at chromosome 9p21. Arterioscler. Thromb. Vasc. Biol. 30, 620 – 627 Cunnington, M. S., Santibanez Koref, M., Mayosi, B. M., Burn, J., and Keavney, B. (2010) Chromosome 9p21 SNPs associated with multiple disease phenotypes correlate with ANRIL expression. PLoS Genet. 6, e1000899 Shete, S., Hosking, F. J., Robertson, L. B., Dobbins, S. E., Sanson, M., Malmer, B., Simon, M., Marie, Y., Boisselier, B., Delattre, J. Y., Hoang-Xuan, K., El Hallani, S., Idbaih, A., Zelenika, D., Andersson, U., Henriksson, R., Bergenheim, A. T., Feychting, M., Lo¨nn, S., Ahlbom, A., Schramm, J., Linnebank, M., Hemminki, K., Kumar, R., Hepworth, S. J., Price, A., Armstrong, G., Liu, Y., Gu, X., Yu, R., Lau, C., Schoemaker, M., Muir, K., Swerdlow, A., Lathrop, M., Bondy, M., and Houlston, R. S. (2009) Genome-wide association study identifies five susceptibility loci for glioma. Nat. Genet. 41, 899 –904 Stacey, S. N., Sulem, P., Masson, G., Gudjonsson, S. A., Thorleifsson, G., Jakobsdottir, M., Sigurdsson, A., Gudbjartsson, D. F., Sigurgeirsson, B., Benediktsdottir, K.R., Thorisdottir, K., Ragnarsson, R., Scherer, D., Hemminki, K., Rudnai, P., Gurzau, E., Koppova, K., Botella-Estrada, R., Soriano, V., Juberias, P., Saez, B., Gilaberte, Y., Fuentelsaz, V., Corredera, C., Grasa, M., Ho¨iom, V., Lindblom, A., Bonenkamp, J. J., van Rossum, M. M., Aben, K. K., de Vries, E., Santinami, M., Di Mauro, M.G., Maurichi, A., Wendt, J., Hochleitner, P., Pehamberger, H., Gudmundsson, J., Magnusdottir, D. N., Gretarsdottir, S., Holm, H., Steinthorsdottir, V., Frigge, M. L., Blondal, T., Saemundsdottir, J., Bjarnason, H., Kristjansson, K., Bjornsdottir, G., Okamoto, I., Rivoltini, L., Rodolfo, M., Kiemeney, L. A., Hansson, J., Nagore, E., Mayordomo, J. I., Kumar, R.,
The FASEB Journal 䡠 www.fasebj.org
PASMANT ET AL.
18.
19.
20.
21. 22.
Karagas, M. R., Nelson, H. H., Gulcher, J. R., Rafnar, T., Thorsteinsdottir, U., Olafsson, J. H., Kong, A., and Stefansson, K. (2009) New common variants affecting susceptibility to basal cell carcinoma. Nat. Genet. 41, 909 –914 Turnbull, C., Ahmed, S., Morrison, J., Pernet, D., Renwick, A., Maranian, M., Seal, S., Ghoussaini, M., Hines, S., Healey, C. S., Hughes, D., Warren-Perry, M., Tapper, W., Eccles, D., Evans, D. G., Breast Cancer Susceptibility Collaboration (UK), Hooning, M., Schutte, M., van den Ouweland, A., Houlston, R., Ross, G., Langford, C., Pharoah, P. D., Stratton, M. R., Dunning, A.M., Rahman, N., and Easton, D. F. (2010) Genome-wide association study identifies five new breast cancer susceptibility loci. Nat. Genet. 42, 504–507 Bei, J. X., Li, Y., Jia, W. H., Feng, B. J., Zhou, G., Chen, L. Z., Feng, Q. S., Low, H. Q., Zhang, H., He, F., Tai, E. S., Kang, T., Liu, E. T., Liu, J., Zeng, Y. X. (2010) A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. Nat. Genet. 42, 599 – 603 Broadbent, H. M., Peden, J. F., Lorkowski, S., Goel, A., Ongen, H., Green, F., Clarke, R., Collins, R., Franzosi, M. G., Tognoni, G., Seedorf, U., Rust, S., Eriksson, P., Hamsten, A., Farrall, M., and Watkins, H.; Procardis Consortium. (2008) Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum. Mol. Genet. 17, 806 – 814 Sharpless, N. E., and DePinho, R. A. (2007) How stem cells age and why this makes us grow old. Nat. Rev. Mol. Cell. Biol. 8, 703–713 Krishnamurthy, J., Ramsey, M. R., Ligon, K. L., Torrice, C., Koh, A., Bonner-Weir, S., and Sharpless, N. E. (2006) p16INK4a induces an age-dependent decline in islet regenerative potential. Nature 443, 453– 457
ANRIL, A LONG NCRNA HOTSPOT IN GWAS
23.
24.
25. 26.
27. 28. 29. 30.
Yap, K. L., Li, S., Mun ˜ oz-Cabello, A. M., Raguz, S., Zeng, L., Mujtaba, S., Gil, J., Walsh, M. J., and Zhou, M. M. (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 38, 662– 674 Messaoudi-Aubert, S. E., Nicholls, J., Maertens, G. N., Brookes, S., Bernstein, E., and Peters, G. (2010) Role for the MOV10 RNA helicase in polycomb-mediated repression of the INK4a tumor suppressor. Nat. Struct. Mol. Biol. 17, 862– 868 Popov, N., and Gil, J. (2010) Epigenetic regulation of the INK4b-ARF-INK4a locus: in sickness and in health. Epigenetics 5, 686 – 691 Visel, A., Zhu, Y., May, D., Afzal, V., Gong, E., Attanasio, C., Blow, M. J., Cohen, J. C., Rubin, E. M., and Pennacchio, L. A. (2010) Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 464, 409 – 412 Berezikov, E., Cuppen, E., and Plasterk, R. H. (2006) Approaches to microRNA discovery. Nat. Genet. 38(Suppl.), S2–S7 Mercer, T. R., Dinger, M. E., and Mattick, J. S. (2009) Long non-coding RNAs, insights into functions. Nat. Rev. Genet. 10, 155–159 Mattick, J. S. (2009) The genetic signatures of noncoding RNAs. PLoS Genet. 5, e1000459 Manolio, T. A. (2010) Genomic medicine, genomewide association studies and assessment of the risk of disease. N. Engl. J. Med. 363, 166 –176 Received for publication September 2, 2010. Accepted for publication October 7, 2010.
5
