Three-dimensional genomic structure and cohesin occupancy correlates with transcriptional activity during spermatogenesis

Here we generated a high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ Hi-C, RNA-seq and ChIP-seq of CTCF and meiotic cohesins RAD21L and REC8. Spermatogenesis cell populations were isolated by Fluorescence-Activated Cell sorting. Hi-C of isolated populations (spermatogonia, primary spermatocytes at leptonema/zygonema and pachynema/diplonema stage, round spermatids and sperm) and C57BL6 fibroblasts as control. RNA-seq of the same populations except for leptonema/zygonema. ChIP-seq of CTCF, RAD21L and REC8 in pachynema/diplonema cells and round spermatids.