Rat PRDM9 shapes recombination landscapes, duration of meiosis, gametogenesis, and age of fertility

Abstract

Background Vertebrate meiotic recombination events are concentrated in regions (hotspots) that display open chromatin marks, such as trimethylation of lysines 4 and 36 of histone 3 (H3K4me3 and H3K36me3). Mouse and human PRDM9 proteins catalyze H3K4me3 and H3K36me3 and determine hotspot positions, whereas other vertebrates lacking PRDM9 recombine in regions with chromatin already opened for another function, such as gene promoters. While these other vertebrate species lacking PRDM9 remain fertile, inactivation of the mouse Prdm9 gene, which shifts the hotspots to the functional regions (including promoters), typically causes gross fertility reduction; and the reasons for these species differences are not clear. Results We introduced Prdm9 deletions into the Rattus norvegicus genome and generated the first rat genome-wide maps of recombination-initiating double-strand break hotspots. Rat strains carrying the same wild-type Prdm9 allele shared 88% hotspots but strains with different Prdm9 alleles only 3%. After Prdm9 deletion, rat hotspots relocated to functional regions, about 40% to positions corresponding to Prdm9-independent mouse hotspots, including promoters. Despite the hotspot relocation and decreased fertility, Prdm9-deficient rats of the SHR/OlaIpcv strain produced healthy offspring. The percentage of normal pachytene spermatocytes in SHR-Prdm9 mutants was almost double than in the PWD male mouse oligospermic sterile mutants. We previously found a correlation between the crossover rate and sperm presence in mouse Prdm9 mutants. The crossover rate of SHR is more similar to sperm-carrying mutant mice, but it did not fully explain the fertility of the SHR mutants. Besides mild meiotic arrests at rat tubular stages IV (mid-pachytene) and XIV (metaphase), we also detected postmeiotic apoptosis of round spermatids. We found delayed meiosis and age-dependent fertility in both sexes of the SHR mutants. Conclusions We hypothesize that the relative increased fertility of rat versus mouse Prdm9 mutants could be ascribed to extended duration of meiotic prophase I. While rat PRDM9 shapes meiotic recombination landscapes, it is unnecessary for recombination. We suggest that PRDM9 has additional roles in spermatogenesis and speciation—spermatid development and reproductive age—that may help to explain male-specific hybrid sterility.

Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features

“…A possible explanation is that in the absence of the marks made by PRDM9, the machinery responsible for making DSBs defaults to residual sites of H3K4me3 (7) either because the mark causes its recruitment, say through a reader protein, or simply because such regions are more accessible. Consistent with the notion that species lacking PRDM9 rely on other H3K4me3 marks, when Prdm9 is knocked out in B6 mice or SHR rats, ~92% and ~99% of DSBs occur at residual sites of H3K4me3, respectively (6,7). The knockout experiments in mice and rats, alongside the report of a human mother homozygous for a nonfunctional PRDM9 (20), further indicate that in species with a complete PRDM9, there exists an alternative mechanism of recombination that can serve as a backup, albeit a less efficient one (7,8,21).…”

“…The mechanisms that specify the genomic location of hotspots differ among species. In mice, humans, and other mammals, the gene PRDM9 (PR/SET Domain 9) plays a key role (2)(3)(4)(5)(6). In mouse and rat, outside of the pseudoautosomal region (6,7), almost all hotspot locations are determined by PRDM9 binding.…”

Differences in Adipose Gene Expression Profiles between Male and Female Even Reindeer (Rangifer tarandus) in Sakha (Yakutia)

“…PRDM9 is one of the rapidly evolving genes in reindeer and is involved in recombination events and epigenetic modifications [ 51 ]. Moreover, recent studies on mice and rats showed that PRDM9 has important roles in spermatogenesis and male fertility [ 41 , 52 ]. Similarly, other upregulated genes in male samples have diverse functions and may be linked to male infertility or spermatogenic failure ( DDX3Y ), mRNA splicing ( ZRSR2 ), lipid metabolism ( EIF2S3X ), circadian rhythm ( USP9X ), cell cycle regulation ( TXLNG ), and photoreceptor development/function ( NRL ).…”

Robust and Efficient Active Genetics Gene Conversion in the Rat and Mouse

“…Other considerations: During these investigations, we considered other elements of the HDR and crossover recombination pathways that might influence the success of various configurations; recombination hotspots and distances to chromosomal ends might contribute to efficiency. In the Sprague-Dawley rat, no hotspot maps are available; strain-to-strain differences are very large, so data from other strains are not applicable (Mihola et al, 2021). We examined the mouse recombination hotspot map from the c57BL derivative mouse line Hop2 -/- (Smagulova et al, 2011).…”