Prdm9 polymorphism unveils mouse evolutionary tracks

Abstract

PR/SET domain containing 9 (Prdm9) mediates histone modifications such as H3K4me3 and marks hotspots of meiotic recombination. In many mammalian species, the Prdm9 gene is highly polymorphic. Prdm9 polymorphism is assumed to play two critical roles in evolution: to diversify the spectrum of meiotic recombination hotspots and to cause male hybrid sterility, leading to reproductive isolation and speciation. Nevertheless, information about Prdm9 sequences in natural populations is very limited. In this study, we conducted a comprehensive population survey on Prdm9 polymorphism in the house mouse, Mus musculus. Overall M. musculus Prdm9 displays an extraordinarily high level of polymorphism, particularly in regions encoding zinc finger repeats, which recognize recombination hotspots. Prdm9 alleles specific to various M. musculus subspecies dominate in subspecies territories. Moreover, introgression into other subspecies territories was found for highly divergent Prdm9 alleles associated with t-haplotype. The results of our phylogeographical analysis suggest that the requirement for hotspot diversity depends on geographical range and time span in mouse evolution, and that Prdm9 polymorphism has not been maintained by a simple balanced selection in the population of each subspecies.

Keywords: Prdm9; evolution; mouse; polymorphism.

Figure 1.

Polymorphisms in Prdm9 cDNA sequences from inbred mouse strains. Amino acid polymorphism of Prdm9 excluding ZFA is summarized. Full-length cDNA of Prdm9 was sequenced for 12 inbred strains derived from M. musculus and one inbred strain derived from a neighbouring species, M. spretus. Nucleotide sequences of the inbred strains were compared with the C57BL/6J reference sequence (NCBI mm9). The C57BL/10J sequence was identical to the reference. Comparison revealed nucleotide substitutions that lead to 16 amino acid substitutions in total, as well as two insertions and one deletion of an amino acid relative to the reference. No amino acid substitution was observed in the PR/SET domains. Upper arrows indicate positions of amino acid variation. An asterisk (*) indicates an interspecific variation (or variation in B10.D2-TCH/+). All amino acid variations are listed in the table below the diagram of Prdm9 protein. The letters S, I, and D in variant types indicate substitution, insertion, and deletion of an amino acid, respectively.

Figure 2.

Amino acid variation in Prdm9 ZF repeats. (A) Multiple alignment of ZF repeat sequences from inbred strains and wild-captured mice. The alignments were made separately for the first repeat, the internal repeats of the ZFA, and the last repeat, as their degrees of variation are different (see text). The α-helix domain of the ZF is shown at top of the internal repeat. The one-letter code is shown to the left of the repeats. A novel repeat found in this study is indicated by # to the right of the repeat. Amino acid variation at specific positions along aligned ZF repeats are shown in colour. The star on the left side in the first repeat corresponds to those shown in Fig. 3. (B) Multiple alignment of ZF repeats of human PRDM9 based on the publically available data (http://www.ncbi.nlm.nih.gov/nuccore). The format of the alignment is the same as that used for mouse Prdm9.

Figure 3.

ZFA alignment for inbred and wild-captured mice. We first assigned a one-letter coding system to ZFAs (see text), then aligned the ZFA diagrams based on the sequences of classical laboratory strains, wild-derived inbred strains, wild-captured mice, neighbouring species of M. musculus, and t-haplotype bearing mice. Using this code, we easily classified all variant types of ZFA. ZFA boxes are aligned from the N-terminal (left of the diagram) to the C-terminal end of the protein (right of the diagram). The diagrams are categorized into DOM- and CAS-related ZFA variant types (left block), MUS-related ZFA variant type (centre block), and other ZFA types of neighbouring species and t-haplotype (right block). The identification (ID) code for each ZFA diagram is indicated onto the left of the diagram. The names of inbred strains and taxonomy are indicated to the left of the ID codes.

Figure 4.

Phylogeny and phylogeography of Prdm9 ZFAs. (A) Phylogenic tree constructed from 57 Prdm9 ZFAs. The identification codes of ZFA variant types are labelled according to the ZFA diagrams (Fig. 3). The 57 ZFA variant types can be divided into five major groups. The names of inbred strains carrying a given ZFA variant type are shown. (B) Points of collection of wild-captured mice are shown on a world map. Background colours indicate the ranges (territories) of each M. musculus subspecies as follows. Blue, DOM; green, MUS; purple, CAS. The red line in Europe indicates a DOM–MUS hybrid zone, where the two subspecies come into contact. Dashed lines indicate borders between other subspecies. For some species, the border regions are not clear. Japanese wild mice, M. m. molossinus, are a hybrid of two subspecies, MUS and CAS.

Figure 5.

Phylogeny of the Prdm9 intronic sequence (HSR1) and Tcp1. (A) Upper diagram, map of the chromosomal region containing Tcp1 and Prdm9. Lower diagram, view of the exon–intron organization of Prdm9. HSR1 is located in an intron between two exons that encode the PR/SET domain. (B) Phylogenetic tree of Prdm9 HSR1. (C) Phylogenetic tree of Tcp1 sequence in introns 8–11. M. caroli was used as the outgroup for both trees. An asterisk (*) to the right of a strain name (ZFA variant) indicates that the samples are heterozygous for Prdm9 HSR1 (B) and Tcp1 intronic (C) sequences.