| URL: | https://3dgenomics.hzau.edu.cn/chromloops |
| Full name: | a comprehensive database for specific protein-mediated chromatin loops in diverse organisms |
| Description: | Chromatin loops (or chromatin interactions) are important elements of chromatin structures. It can help form interactions between regulatory elements, such as promoters, enhancers, silencers, and insulators, thus regulating spatiotemporal gene expression. The current version of ChromLoops integrated 1030 datasets (366 samples) of 13 species of ChIA-PET, HiChIP and PLAC-Seq, and documented a total of 1,491,416,813 high-quality chromatin loops. In addition, we further annotated chromatin loop anchors (genes or regions) with abundant functional annotations information, including enhancers, silencers, SNPs, QTLs, transcription factor binding sites, alternative splicing information, circRNAs, TWAS, chromatin accessibility information and gene expression information. |
| Year founded: | 2022 |
| Last update: | |
| Version: | v1 |
| Accessibility: |
Accessible
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| Country/Region: | China |
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| University/Institution: | Huazhong Agricultural University |
| Address: | |
| City: | Wuhan |
| Province/State: | Hubei |
| Country/Region: | China |
| Contact name (PI/Team): | Guoliang Li |
| Contact email (PI/Helpdesk): | guoliang.li@mail.hzau.edu.cn |
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ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms. [PMID: 36243984]
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. |