{"doi":"10.1101/2023.11.30.569508","title":"CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline","abstract":"Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution 3D chromatin architecture of male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin contacts on autosomes pre-establish meiosis-specific super-enhancers (SE). These meiotic SE recruit the master transcription factor A-MYB in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 resolves chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB establish the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization enforces epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":401790,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9514,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":282082,"name":"Kazuki Takahashi","orcid":"0000-0001-5924-1376","position":1,"is_corresponding":false},{"id":282081,"name":"So Maezawa","orcid":"0000-0002-9060-2042","position":2,"is_corresponding":false},{"id":884811,"name":"Yasuhisa Munakata","orcid":"0000-0002-5134-0828","position":3,"is_corresponding":false},{"id":282080,"name":"Akihiko Sakashita","orcid":"0000-0002-3398-8436","position":4,"is_corresponding":false},{"id":593409,"name":"N. Kaplan","orcid":"0000-0001-9940-1987","position":5,"is_corresponding":false},{"id":282088,"name":"Satoshi H. Namekawa","orcid":"0000-0002-1052-943X","position":6,"is_corresponding":false},{"id":1178757,"name":"Yuka Kitamura","orcid":"0009-0001-7403-0902","position":0,"is_corresponding":true}],"reference_count":83,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:20:12.316631Z","pmid":"38076840","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}