CRISPR-assisted detection of RNA–protein interactions in living cells

Wenkai Yi; Jingyu Li; Xiaoxuan Zhu; Xi Wang; Ligang Fan; Wenju Sun; Linbu Liao; Jilin Zhang; Xiaoyu Li; Jing Ye; Fulin Chen; Jussi Taipale; Kui Ming Chan; Liang Zhang; Jian Yan

doi:10.1038/s41592-020-0866-0

CRISPR-assisted detection of RNA–protein interactions in living cells

Wenkai Yi, Jingyu Li, Xiaoxuan Zhu, Xi Wang, Ligang Fan, Wenju Sun, Linbu Liao, Jilin Zhang, Xiaoyu Li, Jing Ye, Fulin Chen, Jussi Taipale, Kui Ming Chan^*, Liang Zhang^*, Jian Yan^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

88 Citations (Scopus)

Abstract

We have developed CRISPR-assisted RNA–protein interaction detection method (CARPID), which leverages CRISPR–CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealing the method’s wide applicability in identifying RNA-binding proteins.

Original language	English
Pages (from-to)	685–688
Number of pages	4
Journal	Nature Methods
Volume	17
Issue number	7
Online published	22 Jun 2020
DOIs	https://doi.org/10.1038/s41592-020-0866-0
Publication status	Published - Jul 2020

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title = "CRISPR-assisted detection of RNA–protein interactions in living cells",

abstract = "We have developed CRISPR-assisted RNA–protein interaction detection method (CARPID), which leverages CRISPR–CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealing the method{\textquoteright}s wide applicability in identifying RNA-binding proteins.",

author = "Wenkai Yi and Jingyu Li and Xiaoxuan Zhu and Xi Wang and Ligang Fan and Wenju Sun and Linbu Liao and Jilin Zhang and Xiaoyu Li and Jing Ye and Fulin Chen and Jussi Taipale and Chan, {Kui Ming} and Liang Zhang and Jian Yan",

year = "2020",

month = jul,

doi = "10.1038/s41592-020-0866-0",

language = "English",

volume = "17",

pages = "685–688",

journal = "Nature Methods",

issn = "1548-7091",

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TY - JOUR

T1 - CRISPR-assisted detection of RNA–protein interactions in living cells

AU - Yi, Wenkai

AU - Li, Jingyu

AU - Zhu, Xiaoxuan

AU - Wang, Xi

AU - Fan, Ligang

AU - Sun, Wenju

AU - Liao, Linbu

AU - Zhang, Jilin

AU - Li, Xiaoyu

AU - Ye, Jing

AU - Chen, Fulin

AU - Taipale, Jussi

AU - Chan, Kui Ming

AU - Zhang, Liang

AU - Yan, Jian

PY - 2020/7

Y1 - 2020/7

N2 - We have developed CRISPR-assisted RNA–protein interaction detection method (CARPID), which leverages CRISPR–CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealing the method’s wide applicability in identifying RNA-binding proteins.

AB - We have developed CRISPR-assisted RNA–protein interaction detection method (CARPID), which leverages CRISPR–CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealing the method’s wide applicability in identifying RNA-binding proteins.

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UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-85086739180&origin=recordpage

U2 - 10.1038/s41592-020-0866-0

DO - 10.1038/s41592-020-0866-0

M3 - RGC 21 - Publication in refereed journal

C2 - 32572232

SN - 1548-7091

VL - 17

SP - 685

EP - 688

JO - Nature Methods

JF - Nature Methods

IS - 7

ER -

CRISPR-assisted detection of RNA–protein interactions in living cells

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Author Correction: CRISPR-assisted detection of RNA–protein interactions in living cells

GRF: Deciphering the Molecular Mechanisms of H2BE76K Mutation in Cancer

GRF: Elucidate the Biological Significance of Histone H2BG54D Mutation in Pancreatic Cancer

GRF: Delineating the Function and Regulation of Vangl2 in Epithelial-to-mesenchymal Transition (EMT)

Uncovering the secret of RNA paves the way for drug discovery for Covid-19

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CRISPR-assisted detection of RNA–protein interactions in living cells

Abstract

UN SDGs

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Research output

Author Correction: CRISPR-assisted detection of RNA–protein interactions in living cells

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GRF: Deciphering the Molecular Mechanisms of H2BE76K Mutation in Cancer

GRF: Elucidate the Biological Significance of Histone H2BG54D Mutation in Pancreatic Cancer

GRF: Delineating the Function and Regulation of Vangl2 in Epithelial-to-mesenchymal Transition (EMT)

Press/Media

Uncovering the secret of RNA paves the way for drug discovery for Covid-19

Cite this