TY - JOUR
T1 - CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference
AU - Tian, Shuye
AU - Zhang, Bin
AU - He, Yuhao
AU - Sun, Zhiyuan
AU - Li, Jun
AU - Li, Yisheng
AU - Yi, Hongyang
AU - Zhao, Yan
AU - Zou, Xudong
AU - Li, Yunfei
AU - Cui, Huanhuan
AU - Fang, Liang
AU - Gao, Xin
AU - Hu, Yuhui
AU - Chen, Wei
N1 - 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.
PY - 2022/2/22
Y1 - 2022/2/22
N2 - 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.
AB - 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.
UR - http://hdl.handle.net/10754/675588
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac108/6534354
UR - http://www.scopus.com/inward/record.url?scp=85127730011&partnerID=8YFLogxK
U2 - 10.1093/nar/gkac108
DO - 10.1093/nar/gkac108
M3 - Article
C2 - 35191504
SN - 0305-1048
VL - 50
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - 5
ER -