TY - JOUR
T1 - Multicenter integrated analysis of noncoding CRISPRi screens
AU - Yao, David
AU - Tycko, Josh
AU - Oh, Jin Woo
AU - Bounds, Lexi R.
AU - Gosai, Sager J.
AU - Lataniotis, Lazaros
AU - Mackay-Smith, Ava
AU - Doughty, Benjamin R.
AU - Gabdank, Idan
AU - Schmidt, Henri
AU - Guerrero-Altamirano, Tania
AU - Siklenka, Keith
AU - Guo, Katherine
AU - White, Alexander D.
AU - Youngworth, Ingrid
AU - Andreeva, Kalina
AU - Ren, Xingjie
AU - Barrera, Alejandro
AU - Luo, Yunhai
AU - Yardımcı, Galip Gürkan
AU - Tewhey, Ryan
AU - Kundaje, Anshul
AU - Greenleaf, William J.
AU - Sabeti, Pardis C.
AU - Leslie, Christina
AU - Pritykin, Yuri
AU - Moore, Jill E.
AU - Beer, Michael A.
AU - Gersbach, Charles A.
AU - Reddy, Timothy E.
AU - Shen, Yin
AU - Engreitz, Jesse M.
AU - Bassik, Michael C.
AU - Reilly, Steven K.
N1 - Publisher Copyright:
© The Author(s) 2024. corrected publication 2024.
PY - 2024/4
Y1 - 2024/4
N2 - 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.
AB - 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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U2 - 10.1038/s41592-024-02216-7
DO - 10.1038/s41592-024-02216-7
M3 - Article
AN - SCOPUS:85188106930
SN - 1548-7091
VL - 21
SP - 723
EP - 734
JO - Nature Methods
JF - Nature Methods
IS - 4
ER -