期刊
NATURE
卷 549, 期 7670, 页码 111-+出版社
NATURE RESEARCH
DOI: 10.1038/nature23875
关键词
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资金
- NIH [DP3DK111914-01, R01HG0081410-01, R01HL109102, P50-HG007735]
- Scleroderma Research Foundation
- UCSF Sandler Fellowship
- National Multiple Sclerosis Society grant [CA 1074-A-21]
- Marcus Program in Precision Medicine Innovation
- Career Award for Medical Scientists from the Burroughs Wellcome Fund
- Li Ka Shing Foundation
- IGI-AstraZeneca Postdoctoral Fellowship
- DFG Postdoctoral Fellowship
- NIH S10 Instrumentation Grants [S10RR029668, S10RR027303]
- Diabetes Research Center [NIH P30 DK063720]
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(1-3). 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(4-6), 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)(7) 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 (T(H)17) 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.
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