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Nat Genet. 2019 Sep 9. doi: 10.1038/s41588-019-0494-8. [Epub ahead of print]

A compendium of promoter-centered long-range chromatin interactions in the human genome.

Author information

1
Department of Biological Sciences, KAIST, Daejeon, Korea. ijung@kaist.ac.kr.
2
Ludwig Institute for Cancer Research, La Jolla, CA, USA.
3
University of California, San Diego, Biomedical Sciences Graduate Program, La Jolla, CA, USA.
4
Departments of Cell Biology and Orthopaedic Surgery, Regenerative Next Initiative, Duke University School of Medicine, Durham, NC, USA.
5
Department of Biological Sciences, KAIST, Daejeon, Korea.
6
Department of Bio and Brain Engineering, KAIST, Daejeon, Korea.
7
University of California, San Francisco, San Francisco, CA, USA.
8
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
9
Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
10
Department Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
11
Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
12
Krembil Research Institute, University Health Network, Toronto, and The Hospital for Sick Children, Ontario, Canada.
13
Ludwig Institute for Cancer Research, La Jolla, CA, USA. biren@ucsd.edu.
14
Department of Cellular and Molecular Medicine, Center for Epigenomics, Institute of Genomic Medicine, and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA. biren@ucsd.edu.

Abstract

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.

PMID:
31501517
DOI:
10.1038/s41588-019-0494-8

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