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ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms
Chromatin loops (or chromatin interactions) are important 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 p...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825580/ https://www.ncbi.nlm.nih.gov/pubmed/36243984 http://dx.doi.org/10.1093/nar/gkac893 |
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author | Zhou, Qiangwei Cheng, Sheng Zheng, Shanshan Wang, Zhenji Guan, Pengpeng Zhu, Zhixian Huang, Xingyu Zhou, Cong Li, Guoliang |
author_facet | Zhou, Qiangwei Cheng, Sheng Zheng, Shanshan Wang, Zhenji Guan, Pengpeng Zhu, Zhixian Huang, Xingyu Zhou, Cong Li, Guoliang |
author_sort | Zhou, Qiangwei |
collection | PubMed |
description | Chromatin loops (or chromatin interactions) are important 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 1 491 416 813 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 and 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. |
format | Online Article Text |
id | pubmed-9825580 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98255802023-01-10 ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms Zhou, Qiangwei Cheng, Sheng Zheng, Shanshan Wang, Zhenji Guan, Pengpeng Zhu, Zhixian Huang, Xingyu Zhou, Cong Li, Guoliang Nucleic Acids Res Database Issue Chromatin loops (or chromatin interactions) are important 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 1 491 416 813 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 and 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. Oxford University Press 2022-10-16 /pmc/articles/PMC9825580/ /pubmed/36243984 http://dx.doi.org/10.1093/nar/gkac893 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Zhou, Qiangwei Cheng, Sheng Zheng, Shanshan Wang, Zhenji Guan, Pengpeng Zhu, Zhixian Huang, Xingyu Zhou, Cong Li, Guoliang ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms |
title | ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms |
title_full | ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms |
title_fullStr | ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms |
title_full_unstemmed | ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms |
title_short | ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms |
title_sort | chromloops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825580/ https://www.ncbi.nlm.nih.gov/pubmed/36243984 http://dx.doi.org/10.1093/nar/gkac893 |
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