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In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Wu, Qianxin 
Ferry, Quentin RV 
Baeumler, Toni A 
Michaels, Yale S 
Vitsios, Dimitrios M  ORCID logo  https://orcid.org/0000-0002-8939-5445

Abstract

RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs. We use GenERA to survey the entire regulatory landscape of a 3'UTR, and apply it in a multiplex fashion to analyse combinatorial interactions between sets of miRNA response elements (MREs), providing strong evidence for cooperative activity. We also employ this technology to probe the functionality of an entire MRE network under cellular homeostasis, and show that high-resolution analysis of the GenERA dataset can be used to extract functional features of MREs. This study provides a genome editing-based multiplex strategy for direct functional interrogation of RNA cis-regulatory elements in a native cellular environment.

Description

Keywords

3' Untranslated Regions, Animals, CRISPR-Cas Systems, Clustered Regularly Interspaced Short Palindromic Repeats, Gene Editing, Genome, Humans, MicroRNAs, RNA, Regulatory Sequences, Nucleic Acid, Response Elements

Journal Title

Nat Commun

Conference Name

Journal ISSN

2041-1723
2041-1723

Volume Title

8

Publisher

Springer Science and Business Media LLC
Sponsorship
Medical Research Council (MC_PC_12009)