Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map.

PLoS Biol
Authors
Keywords
Abstract

The application of RNA interference (RNAi) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes. Although RNAi has revolutionized loss-of-function genetic experiments, it has been difficult to systematically assess the prevalence and consequences of off-target effects. The Connectivity Map (CMAP) represents an unprecedented resource to study the gene expression consequences of expressing short hairpin RNAs (shRNAs). Analysis of signatures for over 13,000 shRNAs applied in 9 cell lines revealed that microRNA (miRNA)-like off-target effects of RNAi are far stronger and more pervasive than generally appreciated. We show that mitigating off-target effects is feasible in these datasets via computational methodologies to produce a consensus gene signature (CGS). In addition, we compared RNAi technology to clustered regularly interspaced short palindromic repeat (CRISPR)-based knockout by analysis of 373 single guide RNAs (sgRNAs) in 6 cells lines and show that the on-target efficacies are comparable, but CRISPR technology is far less susceptible to systematic off-target effects. These results will help guide the proper use and analysis of loss-of-function reagents for the determination of gene function.

Year of Publication
2017
Journal
PLoS Biol
Volume
15
Issue
11
Pages
e2003213
Date Published
2017 Nov
ISSN
1545-7885
DOI
10.1371/journal.pbio.2003213
PubMed ID
29190685
PubMed Central ID
PMC5726721
Links
Grant list
U54 HL127366 / HL / NHLBI NIH HHS / United States