Multicenter integrated analysis of noncoding CRISPRi screens

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...

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Bibliographic Details
Published in:	Nature methods Vol. 21; no. 4; pp. 723 - 734
Main Authors:	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, Yardımcı, 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.
Format:	Journal Article
Language:	English
Published:	New York Nature Publishing Group US 01-04-2024 Nature Publishing Group
Subjects:	631/1647/2217 631/208/191/2018 Analysis Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Cell lines Clustered Regularly Interspaced Short Palindromic Repeats - genetics Consortia CRISPR CRISPR-Cas Systems - genetics Genome Genomes Guidelines Humans K562 Cells Life Sciences Proteomics Regulatory mechanisms (biology) Regulatory sequences RNA, Guide, CRISPR-Cas Systems Screening Sieve analysis
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Summary:	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. This analysis provides 108 noncoding CRISPR screens collated by the ENCODE4 consortium and establishes experimental guidelines for future CRISPRi screens characterizing functional cis -regulatory elements.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1548-7091 1548-7105 1548-7105
DOI:	10.1038/s41592-024-02216-7