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Discovery of stimulation-responsive immune enhancers with CRISPR activation

Author

Listed:
  • Dimitre R. Simeonov

    (Biomedical Sciences Graduate Program, University of California
    University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • Benjamin G. Gowen

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Mandy Boontanrart

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Theodore L. Roth

    (Biomedical Sciences Graduate Program, University of California
    University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • John D. Gagnon

    (Biomedical Sciences Graduate Program, University of California
    University of California
    Sandler Asthma Basic Research Center, University of California)

  • Maxwell R. Mumbach

    (Center for Personal Dynamic Regulomes, Stanford University School of Medicine
    Program in Epithelial Biology, Stanford University School of Medicine
    Stanford University School of Medicine)

  • Ansuman T. Satpathy

    (Center for Personal Dynamic Regulomes, Stanford University School of Medicine
    Stanford University School of Medicine)

  • Youjin Lee

    (University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • Nicolas L. Bray

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Alice Y. Chan

    (Diabetes Center, University of California
    University of California)

  • Dmytro S. Lituiev

    (Institute for Human Genetics (IHG), University of California)

  • Michelle L. Nguyen

    (University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • Rachel E. Gate

    (Institute for Human Genetics (IHG), University of California
    Biological and Medical Informatics Graduate Program, University of California)

  • Meena Subramaniam

    (Institute for Human Genetics (IHG), University of California
    Biological and Medical Informatics Graduate Program, University of California)

  • Zhongmei Li

    (University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • Jonathan M. Woo

    (University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • Therese Mitros

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Graham J. Ray

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Gemma L. Curie

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Nicki Naddaf

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Julia S. Chu

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Hong Ma

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Eric Boyer

    (Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • Frederic Van Gool

    (Diabetes Center, University of California)

  • Hailiang Huang

    (Broad Institute of MIT and Harvard
    Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School)

  • Ruize Liu

    (Broad Institute of MIT and Harvard
    Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School)

  • Victoria R. Tobin

    (University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • Kathrin Schumann

    (University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California)

  • Mark J. Daly

    (Broad Institute of MIT and Harvard
    Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School)

  • Kyle K. Farh

    (Illumina Inc., 5200 Illumina Way)

  • K. Mark Ansel

    (University of California
    Sandler Asthma Basic Research Center, University of California)

  • Chun J. Ye

    (Institute for Human Genetics (IHG), University of California)

  • William J. Greenleaf

    (Center for Personal Dynamic Regulomes, Stanford University School of Medicine
    Stanford University School of Medicine
    Stanford University
    Chan Zuckerberg Biohub)

  • Mark S. Anderson

    (Diabetes Center, University of California
    University of California)

  • Jeffrey A. Bluestone

    (Diabetes Center, University of California)

  • Howard Y. Chang

    (Center for Personal Dynamic Regulomes, Stanford University School of Medicine
    Program in Epithelial Biology, Stanford University School of Medicine)

  • Jacob E. Corn

    (Innovative Genomics Institute, University of California
    University of California, Berkeley)

  • Alexander Marson

    (University of California
    Diabetes Center, University of California
    Innovative Genomics Institute, University of California
    Chan Zuckerberg Biohub)

Abstract

The authors use tiled CRISPR activation for functional enhancer discovery across two autoimmunity risk loci, CD69 and IL2RA, and identify elements with features of stimulus-responsive enhancers, including an IL2RA enhancer that harbours a fine-mapped autoimmunity risk variant.

Suggested Citation

  • Dimitre R. Simeonov & Benjamin G. Gowen & Mandy Boontanrart & Theodore L. Roth & John D. Gagnon & Maxwell R. Mumbach & Ansuman T. Satpathy & Youjin Lee & Nicolas L. Bray & Alice Y. Chan & Dmytro S. Li, 2017. "Discovery of stimulation-responsive immune enhancers with CRISPR activation," Nature, Nature, vol. 549(7670), pages 111-115, September.
    • Handle: RePEc:nat:nature:v:549:y:2017:i:7670:d:10.1038_nature23875
    DOI: 10.1038/nature23875
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    Citations

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    Cited by:

    1. B. Edginton-White & A. Maytum & S. G. Kellaway & D. K. Goode & P. Keane & I. Pagnuco & S. A. Assi & L. Ames & M. Clarke & P. N. Cockerill & B. Göttgens & J. B. Cazier & C. Bonifer, 2023. "A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    2. Florence M. Chardon & Troy A. McDiarmid & Nicholas F. Page & Riza M. Daza & Beth K. Martin & Silvia Domcke & Samuel G. Regalado & Jean-Benoît Lalanne & Diego Calderon & Xiaoyi Li & Lea M. Starita & St, 2024. "Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Tian Zhou & Xinyi Zhu & Zhizhong Ye & Yong-Fei Wang & Chao Yao & Ning Xu & Mi Zhou & Jianyang Ma & Yuting Qin & Yiwei Shen & Yuanjia Tang & Zhihua Yin & Hong Xu & Yutong Zhang & Xiaoli Zang & Huihua D, 2022. "Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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