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Multicenter integrated analysis of noncoding CRISPRi screens.
Yao, David; Tycko, Josh; Oh, Jin Woo; Bounds, Lexi R; Gosai, Sager J; Lataniotis, Lazaros; Mackay-Smith, Ava; Doughty, Benjamin R; Gabdank, Idan; Schmidt, Henri; Guerrero-Altamirano, Tania; Siklenka, Keith; Guo, Katherine; White, Alexander D; Youngworth, Ingrid; Andreeva, Kalina; Ren, Xingjie; Barrera, Alejandro; Luo, Yunhai; Yardimci, Galip Gürkan; Tewhey, Ryan; Kundaje, Anshul; Greenleaf, William J; Sabeti, Pardis C; Leslie, Christina; Pritykin, Yuri; Moore, Jill E; Beer, Michael A; Gersbach, Charles A; Reddy, Timothy E; Shen, Yin; Engreitz, Jesse M; Bassik, Michael C; Reilly, Steven K.
Afiliación
  • Yao D; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Tycko J; Department of Genetics, Stanford University, Stanford, CA, USA. joshtycko@hms.harvard.edu.
  • Oh JW; Department of Neurobiology, Harvard Medical School, Boston, MA, USA. joshtycko@hms.harvard.edu.
  • Bounds LR; Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
  • Gosai SJ; Department of Biomedical Engineering, Duke University, Durham, NC, USA.
  • Lataniotis L; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
  • Mackay-Smith A; Broad Institute of Harvard & MIT, Cambridge, MA, USA.
  • Doughty BR; Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA.
  • Gabdank I; Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA.
  • Schmidt H; Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA.
  • Guerrero-Altamirano T; University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA.
  • Siklenka K; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Guo K; Department of Genetics, Stanford University, Stanford, CA, USA.
  • White AD; Department of Computer Science, Princeton University, Princeton, NJ, USA.
  • Youngworth I; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Andreeva K; University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA.
  • Ren X; Department of Biology, Duke University, Durham, NC, USA.
  • Barrera A; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
  • Luo Y; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA.
  • Yardimci GG; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Tewhey R; Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
  • Kundaje A; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Greenleaf WJ; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Sabeti PC; Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA.
  • Leslie C; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
  • Pritykin Y; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA.
  • Moore JE; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Beer MA; Knight Cancer Center, Oregon Health and Science University, Portland, OR, USA.
  • Gersbach CA; The Jackson Laboratory, Bar Harbor, ME, USA.
  • Reddy TE; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Shen Y; Department of Computer Science, Stanford University, Stanford, CA, USA.
  • Engreitz JM; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Bassik MC; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
  • Reilly SK; Department of Applied Physics, Stanford University, Stanford, CA, USA.
Nat Methods ; 21(4): 723-734, 2024 Apr.
Article en En | MEDLINE | ID: mdl-38504114
ABSTRACT
The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas / Sistemas CRISPR-Cas Límite: Humans Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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PubMed Links
Buscar en Google

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas / Sistemas CRISPR-Cas Límite: Humans Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos