{"doi":"10.1101/gr.280648.125","title":"Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation","abstract":"Mitotic chromosomes are considered to be universally folded as loop arrays across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type- or species-specific. We previously reported that CTCF binding in human differentiated cell lines is lost in mitosis, whereas mitotic mouse embryonic stem cells (mESC) display prominent binding at a subset of CTCF sites. Here, we perform footprint ATAC-seq analyses of mESCs, and somatic mouse and human cells, confirming these findings. We then investigate roles of mitotically bookmarked CTCF in prometaphase chromosome organization by Hi-C. We do not find any remaining interphase structures, such as TADs or loops, at bookmarked CTCF sites in mESCs. This suggests that mitotic loop extruders condensin I and II are not blocked by CTCF and, thus, that maintained CTCF binding does not alter mitotic chromosome folding. Lastly, we compare mitotic Hi-C data generated in this study in mouse with public data in human and chicken. We do not find any cell type-specific differences; however, we find a difference between species. The average genomic size of mitotic loops is smaller in chicken (200-300 kb) compared to human (400-600 kb) and especially mouse (1-1.5 Mb). Interestingly, we find that this difference is correlated with the genomic length of q-arms in these species, a finding we confirm by microscopy measurements of chromosome compaction. This suggests that the dimensions of mitotic chromosomes can be modulated through control of loop size by condensins to facilitate species-appropriate shortening of chromosome arms.","journal":"Genome Research","year":2025,"id":555606,"datarank":0.2330456792627137,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.02510152509473008,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.02510152509473008,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":3,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9544,"is_data_producer":true,"deposit_databanks":{"GEO":["GSE249331"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":817825,"name":"A. Nicole Fox","orcid":"0000-0001-5012-9177","position":1,"is_corresponding":false},{"id":1168406,"name":"Inma González","orcid":"0000-0003-2523-499X","position":2,"is_corresponding":false},{"id":1168701,"name":"Amandine Molliex","orcid":null,"position":3,"is_corresponding":false},{"id":1168407,"name":"Thaleia Papadopoulou","orcid":"0000-0002-8445-6093","position":4,"is_corresponding":false},{"id":1168408,"name":"Pablo Navarro","orcid":"0000-0002-2700-6598","position":5,"is_corresponding":false},{"id":11679,"name":"Job Dekker","orcid":"0000-0001-5631-0698","position":6,"is_corresponding":false},{"id":348429,"name":"Marlies E. Oomen","orcid":"0000-0002-2432-3862","position":0,"is_corresponding":true}],"reference_count":78,"raw_metadata":null,"created_at":"2026-07-19T02:54:59.329539Z","pmid":"40480831","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":[]}