OCEAN-C

OCEAN-C maps genome-wide open chromatin interactions by integrating FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing) with Hi-C to identify hubs of accessible cis-regulatory elements and their three-dimensional interaction networks.

Key Features:

• Antibody-Independent Mapping: Uses FAIRE-seq to enrich and isolate open chromatin regions without relying on antibodies or protein-specific immunoprecipitation.
• Integration with Hi-C: Combines FAIRE-seq–derived open chromatin enrichment with Hi-C chromosome conformation capture data to map 3D interactions among accessible regions.
• Detection of Hubs of Open Chromatin Interactions (HOCIs): Identifies HOCIs and reports over 10,000 hubs in human cells composed primarily of active promoters and enhancers bound by numerous DNA-binding proteins.
• Topological Structures: Detects higher-order genome organization including topologically associated domains (TADs) and A/B compartments.
• Association with Gene Expression: Associates chromatin interaction patterns with gene expression levels, highlighting interactions correlated with transcriptional activity.
• Super-Enhancers and Broad H3K4me3 Domains: Detects interactions mediated by super-enhancers and broad H3K4me3 domains that are linked to active transcription.

Scientific Applications:

• Gene regulatory network mapping: Maps regulatory interactions among promoters, enhancers, and other cis-regulatory elements.
• Chromatin architecture analysis: Characterizes three-dimensional genome organization including TADs and A/B compartments.
• Identification of regulatory hubs: Identifies HOCIs that may coordinate transcriptional regulation across multiple loci.
• Linking structure to expression and identity: Correlates interaction hubs, super-enhancers, and broad H3K4me3 domains with gene expression, cell identity, and disease-related regulation.
• Study of cis-regulatory roles: Enables investigation of promoters, enhancers, and other cis-regulatory elements in biological processes and disease contexts.

Methodology:

Integrates FAIRE-seq to enrich/isolate open chromatin regions with Hi-C chromosome conformation capture to map three-dimensional interactions, and identifies HOCIs as well as TADs and A/B compartments.