High resolution maps of chromatin reorganization reveals that CTCF anchors meiotic loops in mice.

When germ cells transition from the mitotic cycle into meiotic prophase I, chromosomes condense into an array of chromatin loops that are required to promote homolog pairing and genetic recombination. To identify the changes in chromosomal conformation, we used a unique nuclei sorting strategy to isolate germ cells at stages ranging from spermatogonia, through the mitotic-to-meiotic transition stages, and up to the end of meiotic prophase I. By performing in-situ Hi-C and Micro-C, we explored the trajectory of chromatin reorganization at the highest temporal and spatial resolution to date. We find that the stereotypical large-scale A and B compartmentalization is lost during meiotic prophase I alongside the loss of topological associating domains (TADs). Still, local sub-compartments and the interactions between regulatory elements were detected and maintained throughout the stages analyzed. This establishes a potential mechanism for how the meiotic chromatin maintains active transcription within a highly structured genome. We isolated a previously unrecognized cell population that has exited the spermatogonia stage yet has not entered the traditionally defined meiotic stage. These cells show a concurrent decline in mitotic cohesion and a rise in meiotic cohesin complexes, initiating meiotic chromatin reorganization. Enhanced Micro-C resolution revealed that, despite the loss of TADs, higher frequency contact between two loci were detectable during meiotic prophase I coinciding with CTCF bound sites suggesting that CTCF sites are anchoring meiotic loops. Furthermore, the localization of CTCF to the meiotic axes and its interaction with meiotic-specific cohesins indicated that these anchors were at the base of loops. Strikingly, we find that double-strand break (DSB) hotspot sequences interact with CTCF bound loci at a high frequency. In summary, our high-resolution data reveals previously unappreciated aspects of mammalian meiotic chromatin organization. Our data indicate that CTCF plays a role in stabilizing cohesin complexes and anchoring meiotic loops. Having a preferred looping point might be an important feature that allows both homologs to have an array of loops in register that in turn would facilitate homology search, homologous pairing and subsequent double-strand break repair.