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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...

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Autores principales: Zhou, Qiangwei, Cheng, Sheng, Zheng, Shanshan, Wang, Zhenji, Guan, Pengpeng, Zhu, Zhixian, Huang, Xingyu, Zhou, Cong, Li, Guoliang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
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.
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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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