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Discovery of stimulation-responsive immune enhancers with CRISPR activation.
Simeonov, Dimitre R; Gowen, Benjamin G; Boontanrart, Mandy; Roth, Theodore L; Gagnon, John D; Mumbach, Maxwell R; Satpathy, Ansuman T; Lee, Youjin; Bray, Nicolas L; Chan, Alice Y; Lituiev, Dmytro S; Nguyen, Michelle L; Gate, Rachel E; Subramaniam, Meena; Li, Zhongmei; Woo, Jonathan M; Mitros, Therese; Ray, Graham J; Curie, Gemma L; Naddaf, Nicki; Chu, Julia S; Ma, Hong; Boyer, Eric; Van Gool, Frederic; Huang, Hailiang; Liu, Ruize; Tobin, Victoria R; Schumann, Kathrin; Daly, Mark J; Farh, Kyle K; Ansel, K Mark; Ye, Chun J; Greenleaf, William J; Anderson, Mark S; Bluestone, Jeffrey A; Chang, Howard Y; Corn, Jacob E; Marson, Alexander.
Afiliação
  • Simeonov DR; Biomedical Sciences Graduate Program, University of California, San Francisco, California 94143, USA.
  • Gowen BG; Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA.
  • Boontanrart M; Diabetes Center, University of California, San Francisco, California 94143, USA.
  • Roth TL; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
  • Gagnon JD; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
  • Mumbach MR; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
  • Satpathy AT; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
  • Lee Y; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
  • Bray NL; Biomedical Sciences Graduate Program, University of California, San Francisco, California 94143, USA.
  • Chan AY; Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA.
  • Lituiev DS; Diabetes Center, University of California, San Francisco, California 94143, USA.
  • Nguyen ML; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
  • Gate RE; Biomedical Sciences Graduate Program, University of California, San Francisco, California 94143, USA.
  • Subramaniam M; Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA.
  • Li Z; Sandler Asthma Basic Research Center, University of California, San Francisco, California 94143, USA.
  • Woo JM; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA.
  • Mitros T; Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
  • Ray GJ; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
  • Curie GL; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA.
  • Naddaf N; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
  • Chu JS; Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA.
  • Ma H; Diabetes Center, University of California, San Francisco, California 94143, USA.
  • Boyer E; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
  • Van Gool F; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
  • Huang H; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
  • Liu R; Diabetes Center, University of California, San Francisco, California 94143, USA.
  • Tobin VR; Department of Pediatrics, University of California, San Francisco, California 94143, USA.
  • Schumann K; Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California 94143, USA.
  • Daly MJ; Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA.
  • Farh KK; Diabetes Center, University of California, San Francisco, California 94143, USA.
  • Ansel KM; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
  • Ye CJ; Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California 94143, USA.
  • Greenleaf WJ; Biological and Medical Informatics Graduate Program, University of California, San Francisco, California 94158, USA.
  • Anderson MS; Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California 94143, USA.
  • Bluestone JA; Biological and Medical Informatics Graduate Program, University of California, San Francisco, California 94158, USA.
  • Chang HY; Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA.
  • Corn JE; Diabetes Center, University of California, San Francisco, California 94143, USA.
  • Marson A; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.
Nature ; 549(7670): 111-115, 2017 09 07.
Article em En | MEDLINE | ID: mdl-28854172
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.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Autoimunidade / Elementos Facilitadores Genéticos / Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas / Sistemas CRISPR-Cas Limite: Animals / Female / Humans Idioma: En Ano de publicação: 2017 Tipo de documento: Article
Texto completo
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XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Autoimunidade / Elementos Facilitadores Genéticos / Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas / Sistemas CRISPR-Cas Limite: Animals / Female / Humans Idioma: En Ano de publicação: 2017 Tipo de documento: Article