{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T02:49:03Z","timestamp":1773974943058,"version":"3.50.1"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T00:00:00Z","timestamp":1665878400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFC2701201"],"award-info":[{"award-number":["2021YFC2701201"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970590"],"award-info":[{"award-number":["31970590"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Chromatin loops (or chromatin interactions) are\u00a0important elements of chromatin structures. Disruption of chromatin loops is associated with many diseases, such as cancer and polydactyly. A few methods, including ChIA-PET, HiChIP and PLAC-Seq, have been proposed to detect high-resolution, specific protein-mediated chromatin loops. With rapid progress in 3D genomic research, ChIA-PET, HiChIP and PLAC-Seq datasets continue to accumulate, and effective collection and processing for these datasets are urgently needed. Here, we developed a comprehensive, multispecies and specific protein-mediated chromatin loop database (ChromLoops, https:\/\/3dgenomics.hzau.edu.cn\/chromloops), which integrated 1030 ChIA-PET, HiChIP and PLAC-Seq datasets from 13 species, and documented 1\u00a0491 416 813 high-quality chromatin loops. We annotated genes and regions overlapping with chromatin loop anchors with rich functional annotations, such as regulatory elements (enhancers, super-enhancers and silencers), variations (common SNPs, somatic SNPs\u00a0and eQTLs), and transcription factor binding sites. Moreover, we identified genes with high-frequency chromatin interactions in the collected species. In particular, we identified genes with high-frequency interactions in cancer samples. We hope that ChromLoops will provide a new platform for studying chromatin interaction regulation in relation to biological processes and disease.<\/jats:p>","DOI":"10.1093\/nar\/gkac893","type":"journal-article","created":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T10:07:03Z","timestamp":1665914823000},"page":"D57-D69","source":"Crossref","is-referenced-by-count":19,"title":["ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7948-177X","authenticated-orcid":false,"given":"Qiangwei","family":"Zhou","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sheng","family":"Cheng","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shanshan","family":"Zheng","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenji","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengpeng","family":"Guan","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhixian","family":"Zhu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingyu","family":"Huang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cong","family":"Zhou","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1601-6640","authenticated-orcid":false,"given":"Guoliang","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,16]]},"reference":[{"key":"2023010804272141800_B1","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1093\/hmg\/ddg180","article-title":"A long-range shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly","volume":"12","author":"Lettice","year":"2003","journal-title":"Hum. Mol. Genet."},{"key":"2023010804272141800_B2","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nature08451","article-title":"Genomic views of distant-acting enhancers","volume":"461","author":"Visel","year":"2009","journal-title":"Nature"},{"key":"2023010804272141800_B3","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1038\/ng.2971","article-title":"Long-range enhancers regulating myc expression are required for normal facial morphogenesis","volume":"46","author":"Uslu","year":"2014","journal-title":"Nat. Genet."},{"key":"2023010804272141800_B4","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1038\/s41588-020-0578-5","article-title":"Systematic identification of silencers in human cells","volume":"52","author":"Pang","year":"2020","journal-title":"Nat. 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Res."},{"key":"2023010804272141800_B32","first-page":"D198","article-title":"SEA version 3.0: a comprehensive extension and update of the super-enhancer archive","volume":"48","author":"Chen","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2023010804272141800_B33","doi-asserted-by":"crossref","first-page":"D164","DOI":"10.1093\/nar\/gkv1002","article-title":"dbSUPER: a database of super-enhancers in mouse and human genome","volume":"44","author":"Khan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023010804272141800_B34","doi-asserted-by":"crossref","first-page":"D88","DOI":"10.1093\/nar\/gkl822","article-title":"VISTA enhancer Browser\u2013a database of tissue-specific human enhancers","volume":"35","author":"Visel","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023010804272141800_B35","doi-asserted-by":"crossref","first-page":"D221","DOI":"10.1093\/nar\/gkaa839","article-title":"SilencerDB: a comprehensive database of 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