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

Abstract

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.

Overexpressed KCNK1 regulates potassium channels affecting molecular mechanisms and biological pathways in bladder cancer

“…Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) and ChIP-seq of multiple histone modifications were derived from Cistrome Data Browser. Chromloops is a novel database that aggregates a large number of PLAC-seq, ChIA-PET, and HiChIP datasets, which are often used in studies of chromatin interaction regulation [ 26 ]. In this study, the ChIA-PET dataset of Homo sapiens HT-1197 was included and RAD21 was identified as a ChIP-seq marker.…”

Novel DNA methylation biomarkers in enhancer regions with chromatin interactions for diagnosis of non‐small‐cell lung cancer

“…Several well‐established databases, such as ChromLoops 40 and 3DIV, 41 offer a wealth of information on chromatin interactions in various types of cancer. By combining chromatin interactions and DNA methylation information of enhancer regions, we anticipate the emergence of increasingly accurate DNA methylation biomarkers in the future.…”

The dynamic role of cohesin in maintaining human genome architecture

“…[117,118] Selected recently published databases provide a platform to study chromatin interactions, regulations and organisations. Such Example is ChromLoops [119] [https://3dgenomics.hzau.edu.cn/chromloops],…”

“…[ 117,118 ] Selected recently published databases provide a platform to study chromatin interactions, regulations and organisations. Such Example is ChromLoops [ 119 ] [https://3dgenomics.hzau.edu.cn/chromloops], an integrated dataset for high‐quality chromatin loops from 1030 datasets across 366 samples from 13 species from ChIA‐PET, HiChIP and PLAC‐Seq datasets. HiChIPdb [ 120 ] [http://health.tsinghua.edu.cn/hichipdb/] contains more than 260 million HiChIP interactions from 200 HiChIP experiments for 208 cell type at variable 1/5/10/50 kb resolution processed by FitHiChIP [ 121 ] and Hichipper [ 122 ] computational pipeline for loop calling.…”