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A compendium of promoter-centered long-range chromatin interactions in the human genome
Open accessAbstract
A large number of putative cis-regulatory sequences have been annotated in the human genome, but the genes they control remain poorly defined. To bridge this gap, we generate maps of long-range chromatin interactions centered on 18,943 well-annotated promoters for protein-coding genes in 27 human cell/tissue types. We use this information to infer the target genes of 70,329 candidate regulatory elements and suggest potential regulatory function for 27,325 noncoding sequence variants associated with 2,117 physiological traits and diseases. Integrative analysis of these promoter-centered interactome maps reveals widespread enhancer-like promoters involved in gene regulation and common molecular pathways underlying distinct groups of human traits and diseases.
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“consistent with the previous findings that multiple enhancers can interact with one promoter3,7.”
From Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders (2021) · cites this paper as [7]
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Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Self-citationA 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Self-citationIntegrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368
Self-citationThe Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
The GTEx Consortium, Ardlie, K. G., Deluca, D. S., Segrè, A. V., Sullivan, T. J., Young, T. R., Gelfand, E. T., Trowbridge, C. A., Maller, J. B., Tukiainen, T., et al. (2015) · Science · doi:10.1126/science.1262110 · Cited by 5,062
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143
Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1229 · Cited by 2,707
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Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J. D., Conte, M., Gorkin, D. U., Yu, M., et al. (2020) · bioRxiv · doi:10.1101/2020.03.21.001693 · Cited by 10
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Wang, H., Yang, J., Zhang, Y., & Wang, J. (2020) · Methods · doi:10.1016/j.ymeth.2020.10.010 · Cited by 12
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Narumi, S., Opitz, R., Nagasaki, K., Muroya, K., Asakura, Y., Adachi, M., Abe, K., Sugisawa, C., Kühnen, P., Ishii, T., et al. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac093 · Cited by 8
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Lin, S., Wu, S., Zhao, W., Fang, Z., Kang, H., Liu, X., Pan, S., Yu, F., Bào, Y., & Jia, P. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad901 · Cited by 8
Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin
Yi, X., Zheng, Z., Xu, H., Zhou, Y., Huang, D., Wang, J., Feng, X., Zhao, K., Fan, X., Zhang, S., et al. (2021) · iScience · doi:10.1016/j.isci.2021.103468 · Cited by 8
Comparison of Capture Hi-C Analytical Pipelines
Aljogol, D., Thompson, I. R., Osborne, C. S., & Mifsud, B. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.786501 · Cited by 8
Groenewoud, D., Shye, A., & Elkon, R. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009908 · Cited by 8
D’Aurizio, R., Catona, O., Pitasi, M., Li, Y. E., Ren, B., & Nicolis, S. K. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23147964 · Cited by 9
Self-citationFIREcaller: Detecting Frequently Interacting Regions from Hi-C DataPreprint
Crowley, C., Yang, Y., Qiu, Y., Hu, B., Abnousi, A., Lipiński, J., Plewczyński, D., Wu, D., Won, H., Ren, B., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/619288 · Cited by 8
Self-citationLee, A., Kim, C., Park, S.-W., Jun, K., Eom, J., Lee, S., Chung, S. J., Rissman, R. A., Chung, J., Masliah, E., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.13.479386 · Cited by 8
Self-citationHe, Y., Xue, Y., Wang, J., Huang, Y., Liu, L., Huang, Y., & Gao, Y. Q. (2023) · Genome Research · doi:10.1101/gr.277737.123 · Cited by 8
Identifying genetic variants associated with chromatin looping and genome function
Bhattacharyya, S., & Ay, F. (2024) · Nature Communications · doi:10.1038/s41467-024-52296-4 · Cited by 8
Eralp, B., & Sefer, E. (2025) · Scientific Reports · doi:10.1038/s41598-025-21746-4 · Cited by 8
Enhancer/gene relationships: Need for more reliable genome-wide reference sets
Hoellinger, T., Mestre, C., Aschard, H., Goff, W. L., Foissac, S., Faraut, T., & Djebali, S. (2023) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2023.1092853 · Cited by 8
Accelerating 3D genomics data analysis with Microcket
Zhao, Y. F., Yang, M., Gong, F., Pan, Y., Hu, M., Qin, P., Lu, L., Lyu, X., & Sun, K. (2024) · Communications Biology · doi:10.1038/s42003-024-06382-4 · Cited by 6
Singh, P., Serizay, J., Couble, J., Cabahug, M. D., Rosa, C., Chen, P. B., Scherf, A., Koszul, R., Baumgarten, S., & Bryant, J. M. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02038-z · Cited by 11
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Yuan, X., Scott, I. C., & Wilson, M. D. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.642975 · Cited by 7
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants
Dong, C., Simonett, S. P., Shin, S., Stapleton, D. S., Schueler, K. L., Churchill, G. A., Lu, L., Liu, X., Jin, F., Li, Y., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02450-8 · Cited by 9
Shi, Z., Xu, J., Niu, L., Shen, W., Yan, S., Tan, Y., Quan, X., Cheung, E. C. W., Huang, K., Chen, Y., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112151 · Cited by 7
Gene prioritization in GWAS loci using multimodal evidencePreprint
Schipper, M., de Leeuw, C., Maciel, B. D. A. P. C., Wightman, D. P., Hubers, N., Boomsma, D. I., O’Donovan, M. C., & Danielle Posthuma, B. (2023) · medRxiv · doi:10.1101/2023.12.23.23300360 · Cited by 7
Wan, J., van Ouwerkerk, A. F., Mouren, J.-C., Heredia, C., Pradel, L. C., Ballester, B., Andrau, J., & Spicuglia, S. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1270 · Cited by 7
Wang, H., Yang, J., Yu, X., Zhang, Y., Qian, J., & Wang, J. (2025) · Nature Communications · doi:10.1038/s41467-025-58674-w · Cited by 7
Species-specific chromatin architecture and neurogenesis mediated by a human enhancer
Mosti, F., Liu, J., Lam, K., Dillon, N. R., Skavicus, S., Kapps, V. A., Gjoni, K., Lee, C.-F., Glidewell, E. N., Heaton, N. S., et al. (2026) · Cell stem cell · doi:10.1016/j.stem.2026.02.009 · Cited by 6
How our brains are built: emerging approaches to understand human-specific features
Moss, N. D., Lollis, D., & Silver, D. L. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102278 · Cited by 7
Metadata
- Authors
- Jung, I., Schmitt, A., Diao, Y., Lee, A. J., Liu, T., Yang, D., Tan, C., Eom, J., Chan, M., Chee, S., Chiang, Z., Kim, C., Masliah, E., Barr, C. L., Li, B., Kuan, S., Kim, D., & Ren, B.
- Affiliations
- Korea Advanced Institute of Science and Technology (KR)
- University of California San Diego (US)
- Duke University (US)
- Ludwig Cancer Research (US)
- University of California, San Francisco (US)
- National Institutes of Health (US)
- University Health Network (CA)
- Corresponding author
- Jung, Inkyung
- Ren, Bing
- ORCID
- Venue
- Nature Genetics
- Published
- 2019-09-09
- Volume
- 51
- Issue
- 10
- Pages
- 1442-1449
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC6778519
- OpenAlex
- W2955994579
- Cited by
- 362
- References
- 41
- Citations by year
- 2026: 32 · 2025: 40 · 2024: 40 · 2023: 45 · 2022: 74 · 2021: 79 · 2020: 49 · 2019: 2
- FWCI
- 17.94
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Ludwig Institute for Cancer Research
- U.S. Department of Health & Human Services | National Institutes of Health (U54HG006997, 1R01ES024984)
- Ministry of Science, ICT and Future Planning (2017R1C1B2008838)
- Ministry of Health and Welfare (HI17C0328)
- SUHF Fellowship is private funding from Suh Kyungbae Foundation (https://www.suhf.org/main/index.do) for young researchers.
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- long-range chromatin interactions, promoter, cis-regulatory elements, non-coding variants, human qualities, disease, gene expression regulation
- MeSH terms
- Chromatin, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Transcription Factors, Genome, Human, Genomics
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