Genome-wide enhancer maps link risk variants to disease genes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-04-07

AUTHORS

Joseph Nasser, Drew T. Bergman, Charles P. Fulco, Philine Guckelberger, Benjamin R. Doughty, Tejal A. Patwardhan, Thouis R. Jones, Tung H. Nguyen, Jacob C. Ulirsch, Fritz Lekschas, Kristy Mualim, Heini M. Natri, Elle M. Weeks, Glen Munson, Michael Kane, Helen Y. Kang, Ang Cui, John P. Ray, Thomas M. Eisenhaure, Ryan L. Collins, Kushal Dey, Hanspeter Pfister, Alkes L. Price, Charles B. Epstein, Anshul Kundaje, Ramnik J. Xavier, Mark J. Daly, Hailiang Huang, Hilary K. Finucane, Nir Hacohen, Eric S. Lander, Jesse M. Engreitz

ABSTRACT

Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complex traits, each of which could reveal insights into the mechanisms of disease1. Many of the underlying causal variants may affect enhancers2,3, but we lack accurate maps of enhancers and their target genes to interpret such variants. We recently developed the activity-by-contact (ABC) model to predict which enhancers regulate which genes and validated the model using CRISPR perturbations in several cell types4. Here we apply this ABC model to create enhancer–gene maps in 131 human cell types and tissues, and use these maps to interpret the functions of GWAS variants. Across 72 diseases and complex traits, ABC links 5,036 GWAS signals to 2,249 unique genes, including a class of 577 genes that appear to influence multiple phenotypes through variants in enhancers that act in different cell types. In inflammatory bowel disease (IBD), causal variants are enriched in predicted enhancers by more than 20-fold in particular cell types such as dendritic cells, and ABC achieves higher precision than other regulatory methods at connecting noncoding variants to target genes. These variant-to-function maps reveal an enhancer that contains an IBD risk variant and that regulates the expression of PPIF to alter the membrane potential of mitochondria in macrophages. Our study reveals principles of genome regulation, identifies genes that affect IBD and provides a resource and generalizable strategy to connect risk variants of common diseases to their molecular and cellular functions. More... »

PAGES

238-243

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  • Journal

    TITLE

    Nature

    ISSUE

    7858

    VOLUME

    593

    Author Affiliations

  • Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Bristol Myers Squibb, Cambridge, MA, USA
  • Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany
  • Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
  • Department of Statistics, Harvard University, Cambridge, MA, USA
  • Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
  • Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
  • BASE Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford University School of Medicine, Stanford, CA, USA
  • Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, USA
  • Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
  • Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
  • Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
  • Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
  • Department of Computer Science, Stanford University, Stanford, CA, USA
  • Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
  • Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
  • Department of Medicine, Harvard Medical School, Boston, MA, USA
  • Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
  • Office of Science and Technology Policy, Executive Office of the President, White House, Washington, DC, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41586-021-03446-x

    DOI

    http://dx.doi.org/10.1038/s41586-021-03446-x

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1136981959

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/33828297


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