Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening

Overview

Journal Nat Protoc

Specialties Biology
Pathology
Science

Date 2017 Mar 24

PMID 28333914

Citations 586

Authors

Julia Joung

Silvana Konermann

Jonathan S Gootenberg

Omar O Abudayyeh

Randall J Platt

Mark D Brigham

Neville E Sanjana

Feng Zhang

Affiliations

Soon will be listed here.

Abstract

Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeats) immune system has been adapted for genome-scale screening by combining Cas9 with pooled guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom- or ready-made guide RNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening. As each screen is unique, we provide guidelines for determining screening parameters and maintaining sufficient coverage. To validate candidate genes identified by the screen, we further describe strategies for confirming the screening phenotype, as well as genetic perturbation, through analysis of indel rate and transcriptional activation. Beginning with library design, a genome-scale screen can be completed in 9-15 weeks, followed by 4-5 weeks of validation.

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