Multicenter Integrated Analysis of Noncoding CRISPRi Screens

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2024 Mar 20

PMID 38504114

Authors

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 Gurkan Yardimci

Ryan 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

Affiliations

Soon will be listed here.

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.

Citing Articles

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An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation.

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