OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks

Genome Biology
Tingting LiCheng Li

Abstract

We develop a method called open chromatin enrichment and network Hi-C (OCEAN-C) for antibody-independent mapping of global open chromatin interactions. By integrating FAIRE-seq and Hi-C, OCEAN-C detects open chromatin interactions enriched by active cis-regulatory elements. We identify more than 10,000 hubs of open chromatin interactions (HOCIs) in human cells, which are mainly active promoters and enhancers bound by many DNA-binding proteins and form interaction networks crucial for gene transcription. In addition to identifying large-scale topological structures, including topologically associated domains and A/B compartments, OCEAN-C can detect HOCI-mediated chromatin interactions that are strongly associated with gene expression, super-enhancers, and broad H3K4me3 domains.

References

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Citations

Dec 19, 2019·Nature Reviews. Genetics·Rieke Kempfer, Ana Pombo
Jul 3, 2020·Epigenetics & Chromatin·Yan ZhangBingtao Hao
Jan 6, 2019·Cell Biology and Toxicology·Siyuan Kong, Yubo Zhang
May 13, 2020·Science China. Life Sciences·Yan Zhang, Guoliang Li
Apr 7, 2020·Science China. Life Sciences·Mengfan LiCheng Li
Feb 10, 2021·The New Phytologist·Liuling PeiMaojun Wang

Datasets Mentioned

BETA
GM12878
cells

Methods Mentioned

BETA
PLAC-seq
Hi-C
FAIRE-seq
ChIP-seq
RNA-seq
ICE
pull-down
PCR
Illumina sequencing

Related Concepts

Chromatin
DNA Helix Destabilizing Proteins
Enhancer Elements, Genetic
Early Promoters, Genetic
Genomics
Histone Code
Cell Line, Tumor
Gene Modules
Body Fluid Compartments
DNA-Binding Proteins

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