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

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.

SUBMITTER: Li T

PROVIDER: S-EPMC5926533 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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

Li Tingting T Jia Lumeng L Cao Yong Y Chen Qing Q Li Cheng C

Genome biology 20180424 1

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 transc ...[more]

PMID: 29690904

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

Project description: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.

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Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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