ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms

• Published in: Nucleic acids research Vol. 51; no. D1; pp. D57 - D69
• Main Authors: Zhou, Qiangwei, Cheng, Sheng, Zheng, Shanshan, Wang, Zhenji, Guan, Pengpeng, Zhu, Zhixian, Huang, Xingyu, Zhou, Cong, Li, Guoliang
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 06-01-2023
• Subjects: Animals; Chromatin - genetics; Chromosomes; Database Issue; Databases, Genetic; Genome; Genomics; Humans; Regulatory Sequences, Nucleic Acid
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkac893

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.