{"doi":"10.1101/gr.269860.120","title":"Chromatin architecture transitions from zebrafish sperm through early embryogenesis","abstract":"Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish gamete cells to discern whether it either resembles or informs early pre-ZGA zebrafish embryo chromatin architecture. First, we assessed the higher-order architecture through advanced low-cell in situ Hi-C. The structure of zebrafish sperm, packaged by histones, lacks topological associated domains and instead displays \"hinge-like\" domains of ∼150 kb that repeat every 1-2 Mbs, suggesting a condensed repeating structure resembling mitotic chromosomes. The pre-ZGA embryos lacked chromosomal structure, in contrast to prior work, and only developed structure post-ZGA. During post-ZGA, we find chromatin architecture beginning to form at small contact domains of a median length of ∼90 kb. These small contact domains are established at enhancers, including super-enhancers, and chemical inhibition of Ep300a (p300) and Crebbpa (CBP) activity, lowering histone H3K27ac, but not transcription inhibition, diminishes these contacts. Together, this study reveals hinge-like domains in histone-packaged zebrafish sperm chromatin and determines that the initial formation of high-order chromatin architecture in zebrafish embryos occurs after ZGA primarily at enhancers bearing high H3K27ac.","journal":"Genome Research","year":2021,"id":212817,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":99,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9208,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":803905,"name":"Yixuan Guo","orcid":"0000-0003-1940-1931","position":1,"is_corresponding":false},{"id":248545,"name":"Mengyao Tan","orcid":null,"position":2,"is_corresponding":false},{"id":803906,"name":"Ryohei Nakamura","orcid":"0000-0002-7812-8034","position":3,"is_corresponding":false},{"id":561653,"name":"Dana Klatt Shaw","orcid":"0000-0003-3299-3070","position":4,"is_corresponding":false},{"id":803907,"name":"Noèlia Díaz","orcid":"0000-0002-0319-3448","position":5,"is_corresponding":false},{"id":804654,"name":"Aneasha F. Whittaker-Tademy","orcid":null,"position":6,"is_corresponding":false},{"id":18708,"name":"Neva C. Durand","orcid":"0009-0006-5647-2623","position":7,"is_corresponding":false},{"id":18710,"name":"Erez Lieberman Aiden","orcid":"0000-0003-0634-6486","position":8,"is_corresponding":false},{"id":175601,"name":"Juan M. Vaquerizas","orcid":"0000-0002-6583-6541","position":9,"is_corresponding":false},{"id":561656,"name":"David J. Grunwald","orcid":"0000-0002-6784-6647","position":10,"is_corresponding":false},{"id":803908,"name":"Hiroyuki Takeda","orcid":"0000-0002-7932-6358","position":11,"is_corresponding":false},{"id":233430,"name":"Bradley R. Cairns","orcid":"0000-0002-9864-8811","position":12,"is_corresponding":false},{"id":804653,"name":"Candice L. Wike","orcid":null,"position":0,"is_corresponding":true}],"reference_count":63,"raw_metadata":null,"created_at":"2026-07-18T23:52:31.378994Z","pmid":"34006569","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":[]}