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Nature. 2017 Sep 7;549(7670):111-115. doi: 10.1038/nature23875. Epub 2017 Aug 30.

Discovery of stimulation-responsive immune enhancers with CRISPR activation.

Simeonov DR1,2,3,4, Gowen BG4,5, Boontanrart M4,5, Roth TL1,2,3,4, Gagnon JD1,2,6, Mumbach MR7,8,9, Satpathy AT7,9, Lee Y2,3,4, Bray NL4,5, Chan AY3,10, Lituiev DS11, Nguyen ML2,3,4, Gate RE11,12, Subramaniam M11,12, Li Z2,3,4, Woo JM2,3,4, Mitros T4,5, Ray GJ4,5, Curie GL4,5, Naddaf N4,5, Chu JS4,5, Ma H4,5, Boyer E3,4, Van Gool F3, Huang H13,14, Liu R13,14, Tobin VR2,3,4, Schumann K2,3,4, Daly MJ13,14, Farh KK15, Ansel KM2,6, Ye CJ11, Greenleaf WJ7,9,16,17, Anderson MS3,18, Bluestone JA3, Chang HY7,8, Corn JE4,5, Marson A2,3,4,17,18,19.

Author information

1
Biomedical Sciences Graduate Program, University of California, San Francisco, California 94143, USA.
2
Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA.
3
Diabetes Center, University of California, San Francisco, California 94143, USA.
4
Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
5
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
6
Sandler Asthma Basic Research Center, University of California, San Francisco, California 94143, USA.
7
Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA.
8
Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
9
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
10
Department of Pediatrics, University of California, San Francisco, California 94143, USA.
11
Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California 94143, USA.
12
Biological and Medical Informatics Graduate Program, University of California, San Francisco, California 94158, USA.
13
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
14
Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
15
Illumina Inc., 5200 Illumina Way, San Diego, California 92122, USA.
16
Department of Applied Physics, Stanford University, Stanford, California 94025, USA.
17
Chan Zuckerberg Biohub, San Francisco, California 94158, USA.
18
Department of Medicine, University of California, San Francisco, California 94143, USA.
19
UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA.

Abstract

The majority of genetic variants associated with common human diseases map to enhancers, non-coding elements that shape cell-type-specific transcriptional programs and responses to extracellular cues. Systematic mapping of functional enhancers and their biological contexts is required to understand the mechanisms by which variation in non-coding genetic sequences contributes to disease. Functional enhancers can be mapped by genomic sequence disruption, but this approach is limited to the subset of enhancers that are necessary in the particular cellular context being studied. We hypothesized that recruitment of a strong transcriptional activator to an enhancer would be sufficient to drive target gene expression, even if that enhancer was not currently active in the assayed cells. Here we describe a discovery platform that can identify stimulus-responsive enhancers for a target gene independent of stimulus exposure. We used tiled CRISPR activation (CRISPRa) to synthetically recruit a transcriptional activator to sites across large genomic regions (more than 100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA. We identified several CRISPRa-responsive elements with chromatin features of stimulus-responsive enhancers, including an IL2RA enhancer that harbours an autoimmunity risk variant. Using engineered mouse models, we found that sequence perturbation of the disease-associated Il2ra enhancer did not entirely block Il2ra expression, but rather delayed the timing of gene activation in response to specific extracellular signals. Enhancer deletion skewed polarization of naive T cells towards a pro-inflammatory T helper (TH17) cell state and away from a regulatory T cell state. This integrated approach identifies functional enhancers and reveals how non-coding variation associated with human immune dysfunction alters context-specific gene programs.

PMID:
28854172
PMCID:
PMC5675716
DOI:
10.1038/nature23875
[Indexed for MEDLINE]
Free PMC Article

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