test for a sequence binding PRDM9-like protein in Drosophila pseudoobscura using all zinc finger proteins and predicting their sequence motifs using previously ...
Sequence features do not mediate changes in recombination rate within or between species of Drosophila Caiti Smukowski and Mohamed Noor Department of Biology, Duke University, Durham, NC Recombination rate is variable Recombination rate variation in the Drosophila pseudoobscura species group Fine-scale map (20kb scale)
Sequence motifs do not explain recombination rate variation within or between species Within species
Recombination rates are variable across the genome, within and between species.
D. miranda D. pseudoobscura Flagstaff D. pseudoobscura Pikes Peak
Broad-scale map (180kb scale)
The fine-scale map reveals variation undetectable in the broad scale map. D. miranda recombination rate is ~1.3x higher than its close relative D. pseudoobscura.
Human PRDM9 motif
A representative Drosophila motif p=0.7814 r= 0.024495
p=0.0008 r=0.238325
Recombination rate (cM/Mb)
Recombination rate (cM/Mb)
D. pseudoobscura Flagstaff
We find no evidence of a PRDM9 like protein functioning in a sequence-specific way within species of the D. pseudoobscura group, even when examined at a cM scale similar to human studies.
Occurrence of sequence motif
Chromosome 2 (Mb)
From McGaugh, Smukowski, et. al, in review.
How is this variation determined? (1) From Oliver et al. 2009
(2)
(3)
In humans and mice, the zinc finger protein PRDM9 determines the distribution of recombination hotspots. The SET domain modifies histones with a meiosis specific H3K4me3 mark. The triangles (highlighted in yellow) represent a series of zinc fingers. A zinc finger is a protein domain consisting of two β-sheets and an α-helix. Amino acids at positions -1, 3, and 6 in relation to the start of the α-helix bind DNA. Zinc fingers often bind DNA in tandem, forming a sequence motif. For example, human PRDM9 binds the 13-mer degenerate motif: CCNCCNTNNCCNC. This motif is enriched in human recombination hotspots.
Is a PRDM9-like protein conserved across taxa? RED : PRDM9 present, under rapid positive selection GRAY : missing PRDM9, assumed no recombination hotspots BLACK : PRDM9 present, but not under positive selection
But is there another protein that functions in a similar way? We can test for a sequence binding PRDM9-like protein in Drosophila pseudoobscura using all zinc finger proteins and predicting their sequence motifs using previously developed algorithms (e.g., Workman et al. 2005). Motif Prediction
Between species We identified zinc finger proteins that differed in the amino acid binding residues between D. pseudoobscura and D. miranda and generated predicted sequence motifs for these proteins. We then looked at associations between D. miranda predicted motifs and D. miranda recombination rates and compared this to D. miranda predicted motifs and D. pseudoobscura recombination. (see figure on right). A stronger association within species would suggest that the protein influences recombination rate.
There were no proteins more strongly correlated with recombination rate within species than between species.
What about other motifs or sequence features? The motif recently identified in D. melanogaster (GTGGAAA) by Miller et al. (2012), was not associated with recombination rate at either scale in D. pseudoobscura. Variation in GC content among windows within species had ephemeral associations with recombination rate. Differences in GC content, simple repeats, nucleotide diversity, and nucleotide divergence were not associated with changes in recombination rate between D. pseudoobscura and D. miranda.
Conclusions No evidence for sequence based features mediating recombination in the D. pseudoobscura species group Drosophila are thought to lack hotspots typical in humans and yeast
Singh et al. 2009
Recombination rate variation in the 1.2 Mb white-echinus region in D. melanogaster
From Kaplan et al. 2005
From Ponting, 2011
The protein PRDM9 is nonfunctional in dogs, and no homolog is identifiable in many species, including Drosophila.
We identified sequence motifs for all zinc finger proteins in D. pseudoobscura, then identified their occurrence in intervals of known recombination (~180 kb scale, ~20 kb scale) and tested for an association with recombination rate.
Predicted sequence motif for trade embargo (trem)
Predicted sequence motif for Prdm9
Drosophila differ from yeast and mammals in several key components of meiosis
Winckler et al. 2005
Recombination rate variation in two human populations and chimpanzee in 0.5 Mb region
From Schurko & Logsdon 2008
Drosophila are missing several genes crucial for recombination in other organisms
Perhaps Drosophila have a different recombination initiation system than mammals and yeast Works Cited Kaplan, T., N. Friedman, et al. (2005). "Ab initio prediction of transcription factor targets using structural knowledge." PLoS Comput Biol 1(1).♦ McGaugh, S., C. Smukowski, et al. (2012). “Recombination in Drosophila modulates selection’s effect on linked sites.” In review. ♦ Miller DE, Takeo S, Nandanan K, Paulson A, Gogol MM, et al. (2012) A whole-chromosome analysis of meiotic recombination in Drosophila melanogaster. G3: Genes, Genomes, Genetics 2: 249-260. ♦ Oliver, P. L., L. Goodstadt, et al. (2009). "Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa." Plos Genetics 5(12). ♦ Ponting CP (2011) What are the genomic drivers of the rapid evolution of PRDM9? Trends in Genetics 27: 165-171. ♦ Schurko AM, Logsdon JM (2008) Using a meiosis detection toolkit to investigate ancient asexual "scandals" and the evolution of sex. Bioessays 30: 579-589. ♦ Singh, N. D., C. F. Aquadro, et al. (2009). "Estimation of Fine-Scale Recombination Intensity Variation in the white-echinus Interval of D-melanogaster." Journal of Molecular Evolution 69(1): 42-53. ♦ Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE et al (2005). Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308(5718): 107-111. ♦ Workman, C. T., Y. T. Yin, et al. (2005). "enoLOGOS: a versatile web tool for energy normalized sequence logos." Nucleic Acids Research 33: W389-W392.
