Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Abstract
Transcriptional control in large genomes often requires looping interactions between distal DNA elements, such as enhancers and target promoters. Current chromosome conformation capture techniques do not offer sufficiently high resolution to interrogate these regulatory interactions on a genomic scale. Here we use Capture Hi-C (CHi-C), an adapted genome conformation assay, to examine the long-range interactions of almost 22,000 promoters in 2 human blood cell types. We identify over 1.6 million shared and cell type-restricted interactions spanning hundreds of kilobases between promoters and distal loci. Transcriptionally active genes contact enhancer-like elements, whereas transcriptionally inactive genes interact with previously uncharacterized elements marked by repressive features that may act as long-range silencers. Finally, we show that interacting loci are enriched for disease-associated SNPs, suggesting how distal mutations may disrupt the regulation of relevant genes. This study provides new insights and accessible tools to dissect the regulatory interactions that underlie normal and aberrant gene regulation.
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Enhancers vastly outnumber promoters in human and mouse genomes, and promoters often contact more than one enhancer in the same cell type.
“Enhancers vastly outnumber promoters in human and mouse genomes [131], and consistently promoters often contact more than one enhancer in the same cell type [141, 243, 278, 279].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [278]
The number of enhancers correlates with the expression level of a gene across cell types.
“the number of enhancers correlates with the expression level of a gene across cell types [243, 278, 279, 349].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [278]
Within the last decade, hematopoietic regulatory elements have been identified that are quite distant from their associated genes, often separated by hundreds of kilobases.
“Within the last decade, however, hematopoietic regulatory elements have been identified that are quite distant from their associated genes, often separated by hundreds of kilobases (Amano et al., 2009; Mifsud et al., 2015; Sanyal et al., 2012; Schoenfelder et al., 2015).”
From Unraveling Hematopoiesis through the Lens of Genomics (2020) · cites this paper as Mifsud et al., 2015
TADs correspond to functional regulatory domains by primarily restricting contact between enhancers and promoters to occur within the same TAD.
“A large body of evidence suggests that TADs correspond to functional regulatory domains by primarily restricting contact between enhancers and promoters to occur within the same TAD3,21–25”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [22]
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Lanchantin, J., & Qi, Y. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa793 · Cited by 17 · see citing works
- Authors
- Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., Herman, B., Happe, S., Higgs, A., LeProust, E., Follows, G. A., Fraser, P., Luscombe, N. M., & Osborne, C. S.
- Affiliations
- Okinawa Institute of Science and Technology Graduate University (JP)
- Babraham Institute (GB)
- The Francis Crick Institute (GB)
- King's College London (GB)
- Agilent Technologies (United States) (US)
- National Health Service (GB)
- Corresponding author
- Luscombe, Nicholas M
- Osborne, Cameron S
- ORCID
- Venue
- Nature Genetics
- Published
- 2015-05-04
- Volume
- 47
- Issue
- 6
- Pages
- 598-606
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W1605145036
- Cited by
- 990
- References
- 39
- Citations by year
- 2026: 40 · 2025: 48 · 2024: 85 · 2023: 66 · 2022: 96 · 2021: 107 · 2020: 130 · 2019: 115 · 2018: 114 · 2017: 93 · 2016: 72 · 2015: 22 · 2014: 1
- FWCI
- 43.30
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Funders
- Wellcome Trust
- Francis Crick Institute (10110)
- Cancer Research UK (16358)
- Biotechnology and Biological Sciences Research Council (BBS/E/B/0000H212, BBS/E/B/000C0405, BBS/E/B/0000M738, BBS/E/B/000C0404)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- Capture Hi-C, chromosome conformation, enhancer-promoter interactions, distal regulatory elements, transcriptional regulation, disease-associated SNPs, chromatin looping
- MeSH terms
- Cell Line, Chromosome Mapping, Epistasis, Genetic, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Genome, Human, Polymorphism, Single Nucleotide, Gene Regulatory Networks
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