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

Genome Biol. 2018 Apr 24;19(1):54. doi: 10.1186/s13059-018-1430-4.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Chromatin / chemistry
  • Chromatin / metabolism*
  • DNA-Binding Proteins / metabolism
  • Enhancer Elements, Genetic
  • Gene Expression Regulation
  • Gene Regulatory Networks*
  • Genomics / methods*
  • Histone Code
  • Humans
  • Promoter Regions, Genetic


  • Chromatin
  • DNA-Binding Proteins