title: Primate evolution of the recombination regulator PRDM9.
abstract: The PRDM9 gene encodes a protein with a highly variable tandem-repeat zinc finger (ZF) DNA-binding domain that plays a key role in determining sequence-specific hotspots of meiotic recombination genome wide. Here we survey the diversity of the PRDM9 ZF domain by sequencing this region in 64 primates from 18 species, revealing 68 unique alleles across all groups. We report ubiquitous positive selection at nucleotide positions corresponding to DNA contact residues and the expansion of ZFs within clades, which confirms the rapid evolution of the ZF domain throughout the primate lineage. Alignment of Neandertal and Denisovan sequences suggests that PRDM9 in archaic hominins was closely related to present-day human alleles that are rare and specific to African populations. In the context of its role in reproduction, our results are consistent with variation in PRDM9 contributing to speciation events in primates.
authors.affiliation: 1] Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, Washington 98105, USA [2].
authors.forename: Jerrod J
authors.initials: JJ
authors.lastname: Schwartz
authors.affiliation: 1] Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, Washington 98105, USA [2].
authors.forename: David J
authors.initials: DJ
authors.lastname: Roach
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, Washington 98105, USA.
authors.forename: James H
authors.initials: JH
authors.lastname: Thomas
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, Washington 98105, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D014644:Genetic Variation; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics*; D008969:Molecular Sequence Data; D011323:Primates / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D016335:Zinc Fingers
chemical_list: D011495:Histone-Lysine N-Methyltransferase; C544431:PRDM9 protein, human