Multicenter integrated analysis of noncoding CRISPRi screens

David Yao, Josh Tycko, Jin Woo Oh, Lexi R. Bounds, Sager J. Gosai, Lazaros Lataniotis, Ava Mackay-Smith, Benjamin R. Doughty, Idan Gabdank, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D. White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan YardımcıRyan Tewhey, Anshul Kundaje, William J. Greenleaf, Pardis C. Sabeti, Christina Leslie, Yuri Pritykin, Jill E. Moore, Michael A. Beer, Charles A. Gersbach, Timothy E. Reddy, Yin Shen, Jesse M. Engreitz, Michael C. Bassik, Steven K. Reilly

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)723-734
Number of pages12
JournalNature Methods
Volume21
Issue number4
DOIs
StatePublished - Apr 2024

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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