Saflund, M. | bioRxiv Science

bioRxiv2026

Evolutionarily labile pachytene piRNAs target an altered set of mRNAs in male hybrids of house mouse subspecies

During male meiosis-I of placental mammals, [~]30-nucleotide pachytene PIWI-interacting RNAs (piRNAs) are expressed to regulate genes required for sperm function. Pachytene piRNA genes evolve rapidly. Whether rapid evolutionary turnover of pachytene piRNAs is under positive selective pressure remains enigmatic. Here, we investigate the evolutionary rate of pachytene piRNA genes over a short evolutionary timescale using geographically isolated mouse subspecies. We demarcate the genes producing postnatal piRNAs in PWK/PhJ and CAST/EiJ. Comparative genomics reveals 16 subspecies-specific pachytene piRNA loci underscoring how labile pachytene piRNA genes are even during short evolutionary timescale. We report a highly abundant CAST/EiJ-specific pi17-CAST locus defying the notion that young pachytene piRNA genes do not produce abundant piRNAs. In fact, male hybrids from the reciprocal crossing C57BL/6J and CAST/EiJ produce pi17-CAST piRNAs almost exclusively from the CAST/EiJ allele suggesting that species-specific nucleotide variants are sufficient to turn a locus into piRNA source. Intriguingly, hybrid males with reduced fertility features retain distinct piRNA-mRNA pairs compared to parents. Our work reveals that rapidly evolving pachytene piRNAs can gain or lose targets in the hybrid males of closely related mammalian species.

evolutionary biology↗

bioRxiv2025

Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice

Meiotic prophase I characterized by homologous recombination and synapsis is an intricate step for spermatogenesis. This process entails extensive changes to chromatin and transcription. Prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation later during meiosis. However, the factor responsible for promoting accessible chromatin at meiotic gene promoters before entry into prophase I is unknown. Here, we discovered that NFYA expressed in pre-meiotic germ cells promotes accessible chromatin at meiotic gene promoters including those regulated by STRA8/MEISON axis. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Functionally, our spatial and single-cell ATAC-seq data revealed that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at meiotic gene promoters. Our study identifies a pioneer role for NFYA in facilitating accessible chromatin at meiotic gene promoters before meiosis, thereby regulating the timely activation of meiotic genetic program.

developmental biology↗