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

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Title
In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering
Author(s)
Qianxin Wu; Quentin R.V Ferry; Toni A. Baeumler; Yale S. Michaels; Dimitrios M. Vitsios; Omer Habib; Roland Arnold; Xiaowei Jiang; Stefano Maio; Bruno R. Steinkraus; Marta Tapia; Paolo Piazza; NI Xu; Georg A. Holländer; Thomas A. Milne; Jin-Soo Kim; Anton J. Enright; Andrew R. Bassett; Tudor A. Fulga
Publication Date
2017-12
Journal
NATURE COMMUNICATIONS, v.8, no.1, pp.2109 -
Publisher
NATURE PUBLISHING GROUP
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. © 2017 The Author(s)
URI
https://pr.ibs.re.kr/handle/8788114/4306
ISSN
2041-1723
Appears in Collections:
Center for Genome Engineering(유전체 교정 연구단) > Journal Papers (저널논문)
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