Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
Open accessAbstract
Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.
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Certain promoters, termed epromoters, can also function as enhancers.
“Finally, evidence from multiple sources including reporter assays [169, 175, 239, 240], CRISPR [240–242], chromatin mapping [243, 244] and population genetics analysis [207, 245] suggests that certain promoters, termed ‘epromoters’, can also function as enhancers (reviewed in [246]).”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [239]
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- Authors
- Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., Sim, H. S., Peh, S. Q., Mulawadi, F. H., Ong, C. T., Orlov, Y. L., Hong, S., Zhang, Z., Landt, S., Raha, D., Euskirchen, G., Wei, C.-L., Ge, W., Wang, H., Davis, C., Fisher-Aylor, K. I., Mortazavi, A., Gerstein, M., Gingeras, T., Wold, B., Sun, Y., Fullwood, M. J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., & Ruan, Y.
- Affiliations
- Genome Institute of Singapore (SG)
- Yale University (US)
- National University of Singapore (SG)
- Stanford Medicine (US)
- University of California, Los Angeles (US)
- Cold Spring Harbor Laboratory (US)
- California Institute of Technology (US)
- Nanyang Technological University (SG)
- Huazhong Agricultural University (CN)
- Corresponding author
- Snyder, Michael
- Ruan, Yijun
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-01
- Volume
- 148
- Issue
- 1-2
- Pages
- 84-98
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3339270
- OpenAlex
- W2011463791
- Cited by
- 1,232
- References
- 8
- Citations by year
- 2026: 25 · 2025: 44 · 2024: 53 · 2023: 79 · 2022: 59 · 2021: 75 · 2020: 100 · 2019: 97 · 2018: 96 · 2017: 118 · 2016: 115 · 2015: 112 · 2014: 92 · 2013: 99 · 2012: 66
- FWCI
- 47.47
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 563 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- National University of Singapore (submittedVersion)
- DR-NTU (Nanyang Technological University) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- Genome Institute of Singapore
- National Institutes of Health
- National Human Genome Research Institute (HG004456, R01HG004456)
- 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
- long-range chromatin interactions, transcriptional regulation, RNA polymerase II, 3D genome organization, enhancer-promoter interactions, cell-specific transcription, ChIA-PET
- MeSH terms
- Chromatin, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Promoter Regions, Genetic, RNA Polymerase II, Transcription, Genetic, Cell Line, Tumor, Chromatin Immunoprecipitation, Genome-Wide Association Study
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