Multi-layered control of chromosomal assembly of the meiotic DNA break machinery

Meiotic DNA double-strand breaks (DSBs) form in chromatin loops that are tethered to chromosome axes. How proteins required for DSB formation in vivo (DSB proteins) assemble on meiotic chromosomes to control non-random DSB distribution remains unsolved. Here we mapped the spatial distributions of all ten DSB proteins that form three complexes (Spo11-Ski8-Rec102-Rec104 [Spo11-core], Rec114-Mei4-Mer2 [RMM], and Mre11-Rad50-Xrs2 [MRX]) in budding yeast and elucidated their functional dependencies with axial proteins Red1 and Hop1. At local levels, our analysis suggests that their axis-associated assembly involves two distinct pathways, Hop1-RMM-MRX and Red1-Spo11 core, whereas Spo11-core alone can bind DSB sites. Red1 also binds DSB sites in a DSB-dependent manner, supporting its critical role in DSB repair. At large scale, all ten DSB proteins and both axial proteins are enriched at DSB-hot domains 20-40 kb wide that correspond to sizes of the axis-loop units. Further analysis at short and long distances suggests that their local assembly, short-range/intra-loop distributions, and long-range/inter-loop distributions are distinctly controlled. Similarly in mouse spermatocytes, MEl4 and a Hop1 homolog HORMAD1 are enriched at DSB-hot domains 1-3 Mb wide, and their long-range distributions are distinctly controlled from their local assembly. Our results elucidate multi-layered mechanisms of chromosomal assembly of the DSB machinery in shaping the DSB landscape in yeast and mouse.