Multi-omics analysis reveals single-cell meiotic hotspot dynamics and epigenomic regulations in female mammals

Meiotic recombination initiates via DNA double-strand breaks (DSBs) at specialized hotspots, while the regulation of meiotic recombination hotspots in females remain elusive due to the scarcity of embryonic stage germ cells (EGCs). Here, we mapped genome-wide active recombination hotspots and estimated their activities in female EGCs at single-cell resolution, revealing the high variability in hotspot usage frequency among individual germ cells. Further investigation of nucleosome positioning and histone modifications at recombination hotspots revealed that PRDM9-mediated open chromatin and flanking H3K4me3 established earlier at high-frequency hotspots compared with less frequently used ones. Unexpectedly, although recombination hotspots usually distributed outside of heterochromatin, H3K9me3 was clearly enriched around hotspots in females, forming a unique H3K4me3/H3K9me3 bivalent state. And we showed that appropriate H3K9me3 level may be required for downstream DSB repairs. Together, our results provided novel understanding about the landscape and epigenomic regulation of recombination hotspots in females. Overall design: We used scATAC-seq, ultra-low-Input native ChIP-seq (ULI-NChIP-seq) and low-input MNase-seq to analyse the change of chromatin accessibility and histone modification profiles in embryonic germ cells and somatic cells in mouse gonads during E13.5 to E16.5.