Refined spatial temporal epigenomic profiling reveals intrinsic connection between PRDM9-mediated H3K4me3 and the fate of double-stranded breaks

Yao Chen,Ruofei Dai,Fei Lan,Siqing Wang,Ruitu Lyu,Yuxuan Zheng,Xi Zhang,Fuchou Tang,Ming-Han Tong,Bowen Rong,Zhen Lin,Nannan Xie

doi:10.1038/s41422-020-0281-1

Abstract

Meiotic recombination is initiated by the formation of double-strand breaks (DSBs), which are repaired as either crossovers (COs) or noncrossovers (NCOs). In most mammals, PRDM9-mediated H3K4me3 controls the nonrandom distribution of DSBs; however, both the timing and mechanism of DSB fate control remain largely undetermined. Here, we generated comprehensive epigenomic profiles of synchronized mouse spermatogenic cells during meiotic prophase I, revealing spatiotemporal and functional relationships between epigenetic factors and meiotic recombination. We find that PRDM9-mediated H3K4me3 at DSB hotspots, coinciding with H3K27ac and H3K36me3, is intimately connected with the fate of the DSB. Our data suggest that the fate decision is likely made at the time of DSB formation: earlier formed DSBs occupy more open chromatins and are much more competent to proceed to a CO fate. Our work highlights an intrinsic connection between PRDM9-mediated H3K4me3 and the fate decision of DSBs, and provides new insight into the control of CO homeostasis.

Highlights

Meiosis is a specialized form of cell division that generates haploid gametes from diploid cells, and is essential for sexual reproduction and evolution[1,2]
We performed ChIP-seq and NOMe-seq on synchronous leptotene and zygotene spermatocytes from Prdm9−/−, Spo11−/−, and Dmc1−/− mice (PRDM9 and SPO11 are required for generation of double-strand breaks (DSBs) during meiosis; DMC1 facilitates the search for homologs) (Supplementary information, Table S1)
Most DSB hotspots (75.7% defined by SPO11-oligo; 84.5% defined by DMC1ssDNA; hereafter DSB hotspots are defined by SPO11-oligo unless explicitly mentioned, see “Materials and Methods” section for more details) overlapped with the newly generated H3K4me[3] peaks, whereas very few hotspots overlapped with the common H3K4me[3] peaks (5.9% defined by SPO11-oligo; 6.6% defined by DMC1-single-stranded DNA (ssDNA)) (Supplementary information, Fig. S2d, e)

Summary

Introduction

Meiosis is a specialized form of cell division that generates haploid gametes from diploid cells, and is essential for sexual reproduction and evolution[1,2]. Fundamental to meiosis is the process of meiotic recombination, which leads to the transmission of new combinations of linked alleles to the generation[1,2]. Following DSB formation, single-stranded DNA (ssDNA) ends are engaged in the process of repair, which results in the loading of RAD51 and DMC11,2,7. This facilitates the search for homologous chromosomes (homologs) in the majority of strand invasion and the formation of single-end invasion strand exchange intermediates (SEIs)[2,8,9,10]. SEIs can be resolved either by synthesis-dependent strand annealing (SDSA) to generate only noncrossover (NCO) recombinants, or by double

Methods

Results

Conclusion