Meiotic cohesin RAD21L shapes 3D genome structure and transcription in the male germline [HiC]

The unique genome organization that chromosome acquired during meiosis is essential for fertility. Yet, the functional implications of the fine-scale spatial 3D genome folding during this process remain poorly understood. Here, we study the impact of RAD21L depletion, a meiosis-specific cohesin subunit, on the 3D genome architecture and gene expression in the male germ line. Employing fluorescence activated cell sorting, chromosome conformation capture and single cell RNA-seq, we found that the absence of RAD21L impairs chromatin organization during meiosis, leading to pronounced alterations of genome compartmentalization and inter- and intra-chromosomal interactions. This conspicuous genome remodelling also disrupts bouquet formation, resulting in increased telomeric interactions between heterologous chromosomes in primary spermatocytes. Importantly, genome remodelling was accompanied by detectable transcriptional dysregulation in spermatogonia and primary spermatocytes, mainly affecting sex chromosomes. Overall, we demonstrate how cohesin shapes the 3D genome reorganization genome-wide during spermatogenesis and influences its transcriptional landscape. Overall design: Germ cell populations from RAD21L-deficient mice were isolated by Fluorescence-Activated Cell Sorting. Hi-C of fibroblasts and isolated populations (spermatogonia and primary spermatocytes at leptotene/zygotene) from RAD21L-deficient mice. Single-cell RNA-seq of whole testes from WT and RAD21L-deficient mice