CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference

Shuye Tian, Bin Zhang, Yuhao He, Zhiyuan Sun, Jun Li, Yisheng Li, Hongyang Yi, Yan Zhao, Xudong Zou, Yunfei Li, Huanhuan Cui, Liang Fang, Xin Gao, Yuhui Hu, Wei Chen

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Alternative polyadenylation (APA) plays an important role in gene regulation. With the recent application of novel sequencing technology in APA profiling, an ever-increasing number of APA genes/sites have been identified. However, the phenotypic relevance of most of these APA isoforms remains elusive, which is largely due to the lack of a convenient genetics tool for APA interference. To address this issue, herein, an efficient method is developed based on the CRISPR-dCas13 system, termed as CRISPR-iPAS. Out of eight different dCas13 proteins, Porphyromonas gulae (Pgu) dCas13b, is identified as the most effective one in blocking the usage of the polyadenylation site (PAS). With guide RNAs targeting at core regulatory elements, dPguCas13b enabled APA regulation of endogenous genes with different APA types, including tandem 3′UTR, alternative terminal exon, as well as intronic PAS. Finally, we demonstrated that the proposed APA perturbation tool could be used to investigate the functional relevance of APA isoforms.
Original languageEnglish (US)
JournalNucleic Acids Research
Volume50
Issue number5
DOIs
StatePublished - Feb 22 2022

Bibliographical note

KAUST Repository Item: Exported on 2022-07-05
Acknowledged KAUST grant number(s): BAS/1/1624-01, FCC/1/1976-23-01, REI/1/4473-01-01, URF/1/4077-01-01, URF/1/4098-01-01
Acknowledgements: Shenzhen Key Laboratory of Gene Regulation and Systems Biology [ZDSYS20200811144002008]; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions [2021SHIBS0002]; National Natural Science Foundation of China [32100431, 31970601]; Shenzhen Science and Technology Program [KQTD20180411143432337]; Office of Research Administration (ORA) at King Abdullah University of Science and Technology (KAUST) [BAS/1/1624-01, FCC/1/1976-23-01, URF/1/4077-01-01, URF/1/4098-01-01, REI/1/4473-01-01]. Funding for open access charge: National Natural Science Foundation of China.

ASJC Scopus subject areas

  • Genetics

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