Vara, CovadongaPaytuví Gallart, AndreuCuartero, YasminaLe Dily, FrançoisGarcia, FranciscaSalvà-Castro, JuditGómez-H, LauraJulià, EvaMoutinho, CatiaAiese Cigliano, RiccardoSanseverino, WalterFornas Carreño, OscarPendás, Alberto M.Heyn, HolgerWaters, Paul D.Marti-Renom, Marc A.Ruiz Herrera, Aurora2019-09-272019-09-272019Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J et al. Three-dimensional genomic structure and cohesin occupancy correlate with transcriptional activity during spermatogenesis. Cell Reports. 2019;28(2):352-67. DOI: 10.1016/j.celrep.2019.06.0372211-1247http://hdl.handle.net/10230/42347Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation.application/pdfeng© 2019 The Author(s).This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).info:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.celrep.2019.06.037info:eu-repo/semantics/openAccess