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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
The accessible chromatin landscape of the human genome
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679
Chromatin architecture reorganization during stem cell differentiation
Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., et al. (2015) · Nature · doi:10.1038/nature14222 · Cited by 1,646
Self-citationThe long-range interaction landscape of gene promoters
Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489
FTO Obesity Variant Circuitry and Adipocyte Browning in Humans
Claussnitzer, M., Dankel, S. N., Kim, K.-H., Quon, G., Meuleman, W., Haugen, C., Glunk, V., Sousa, I. S., Beaudry, J. L., Puviindran, V., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1502214 · Cited by 1,332
Local regulation of gene expression by lncRNA promoters, transcription and splicing
Engreitz, J. M., Haines, J. E., Perez, E. M., Munson, G., Chen, J., Kane, M., McDonel, P. E., Guttman, M., & Lander, E. S. (2016) · Nature · doi:10.1038/nature20149 · Cited by 1,253
Obesity-associated variants within FTO form long-range functional connections with IRX3
Smemo, S., Tena, J. J., Kim, K.-H., Gamazon, E. R., Sakabe, N. J., Gómez-Marín, C., Aneas, I., Credidio, F. L., Sobreira, D. R., Wasserman, N. F., et al. (2014) · Nature · doi:10.1038/nature13138 · Cited by 1,219
A high-resolution map of the three-dimensional chromatin interactome in human cells
Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208
Self-citationLettice, L. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg180 · Cited by 1,164
Javierre, B. M., Burren, O. S., Wilder, S. P., Kreuzhuber, R., Hill, S. M., Sewitz, S., Cairns, J., Wingett, S. W., Várnai, C., Thiecke, M. J., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.037 · Cited by 1,046
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3286 · Cited by 990
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
Tang, Z., Luo, O. J., Li, X., Zheng, M., Zhu, J. J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.024 · Cited by 982
A compendium of chromatin contact maps reveals spatially active regions in the human genome
Schmitt, A. D., Hu, M., Jung, I., Xu, Z., Qiu, Y., Tan, C. L., Li, Y., Lin, S., Lin, Y., Barr, C. L., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.10.061 · Cited by 866
Self-citationChromatin connectivity maps reveal dynamic promoter–enhancer long-range associations
Zhang, Y., Wong, C., Birnbaum, R. Y., Li, G., Favaro, R., Ngan, C. Y., Lim, J., Tai, E., Poh, H. M., Wong, E., et al. (2013) · Nature · doi:10.1038/nature12716 · Cited by 482
The Three-Dimensional Organization of Mammalian Genomes
Yu, M., & Ren, B. (2017) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100616-060531 · Cited by 373
Self-citationRubin, A. J., Barajas, B. C., Furlan-Magaril, M., Lopez-Pajares, V., Mumbach, M. R., Howard, I., Kim, D. S., Boxer, L. D., Cairns, J., Spivakov, M., et al. (2017) · Nature Genetics · doi:10.1038/ng.3935 · Cited by 293
Self-citationGenome-wide characterization of mammalian promoters with distal enhancer functions
Dao, L. T. M., Galindo-Albarrán, A. O., Castro-Mondragon, J. A., Andrieu-Soler, C., Medina-Rivera, A., Souaid, C., Charbonnier, G., Griffon, A., Vanhille, L., Stephen, T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3884 · Cited by 281
The pluripotent genome in three dimensions is shaped around pluripotency factors
de Wit, E., Bouwman, B. A. M., Zhu, Y. K., Klous, P., Splinter, E., Verstegen, M. J. A. M., Krijger, P. H. L., Festuccia, N., Nora, E. P., Welling, M., et al. (2013) · Nature · doi:10.1038/nature12420 · Cited by 278
Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-CPreprint
Dryden, N. H., Broome, L. R., Dudbridge, F., Johnson, N., Orr, N., Schoenfelder, S., Nagano, T., Andrews, S., Wingett, S., Kozarewa, I., et al. (2014) · Genome Research · doi:10.1101/gr.175034.114 · Cited by 261
A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
Diao, Y., Fang, R., Li, B., Meng, Z., Yu, J., Qiu, Y., Lin, K. C., Huang, H., Liu, T., Marina, R. J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4264 · Cited by 259
Self-citationDynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation
Siersbæk, R., Madsen, J. G. S., Javierre, B. M., Nielsen, R., Bagge, E. K., Cairns, J., Wingett, S. W., Traynor, S., Spivakov, M., Fraser, P., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.010 · Cited by 243
High-throughput mapping of regulatory DNA
Rajagopal, N., Srinivasan, S., Kooshesh, K., Guo, Y., Edwards, M. D., Banerjee, B., Syed, T., Emons, B. J. M., Gifford, D. K., & Sherwood, R. I. (2016) · Nature Biotechnology · doi:10.1038/nbt.3468 · Cited by 238
Integrative analysis of haplotype-resolved epigenomes across human tissues
Leung, D., Jung, I., Rajagopal, N., Schmitt, A. D., Selvaraj, S., Lee, A. Y., Yen, C., Lin, S., Lin, Y., Qiu, Y., et al. (2015) · Nature · doi:10.1038/nature14217 · Cited by 228
Self-citationCapture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
Jäger, R., Migliorini, G., Henrion, M., Kandaswamy, R., Speedy, H. E., Heindl, A., Whiffin, N., Carnicer, M. J., Broome, L. R., Dryden, N. H., et al. (2015) · Nature Communications · doi:10.1038/ncomms7178 · Cited by 216
Martin, P., McGovern, A., Orozco, G., Duffus, K., Yarwood, A., Schoenfelder, S., Cooper, N. J., Barton, A., Wallace, C., Fraser, P., et al. (2015) · Nature Communications · doi:10.1038/ncomms10069 · Cited by 213
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
Freire-Pritchett, P., Schoenfelder, S., Várnai, C., Wingett, S. W., Cairns, J., Collier, A. J., García-Vílchez, R., Furlan-Magaril, M., Osborne, C. S., Fraser, P., et al. (2017) · eLife · doi:10.7554/elife.21926 · Cited by 161
Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Sahlén, P., Abdullayev, I., Ramsköld, D., Matskova, L. V., Rilakovic, N., Lötstedt, B., Albert, T. J., Lundeberg, J., & Sandberg, R. (2015) · Genome biology · doi:10.1186/s13059-015-0727-9 · Cited by 139
Long-range enhancers regulating Myc expression are required for normal facial morphogenesis
Uslu, V. V., Petretich, M., Ruf, S., Langenfeld, K., Fonseca, N. A., Marioni, J. C., & Spitz, F. (2014) · Nature Genetics · doi:10.1038/ng.2971 · Cited by 133
3DIV: A 3D-genome Interaction Viewer and database
Yang, D., Jang, I., Choi, J., Kim, M.-S., Lee, A., Kim, H.-W., Eom, J., Kim, D., Jung, I., & Lee, B.-W. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1017 · Cited by 123
Self-citationPromoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
Orlando, G., Law, P., Cornish, A. J., Dobbins, S. E., Chubb, D., Broderick, P., Litchfield, K., Hariri, F., Pastinen, T., Osborne, C. S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0211-z · Cited by 74
Richard, M., Drouin, R., & Beaulieu, A. D. (1998) · Genomics · doi:10.1006/geno.1998.5480 · Cited by 73
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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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