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

doi:10.1093/nar/gkac108

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 journal › Article › peer-review

13 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 language	English (US)
Journal	Nucleic Acids Research
Volume	50
Issue number	5
DOIs	https://doi.org/10.1093/nar/gkac108
State	Published - 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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10.1093/nar/gkac108

https://repository.kaust.edu.sa/bitstream/10754/675588/1/gkac108.pdf

Cite this

@article{ec27844db20945bd81c7c7d57ac20bd9,

title = "CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference",

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.",

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

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.",

year = "2022",

month = feb,

day = "22",

doi = "10.1093/nar/gkac108",

language = "English (US)",

volume = "50",

journal = "Nucleic Acids Research",

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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.

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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 -

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

Abstract

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