Capturing the interactome of newly transcribed RNA

Xichen Bao; Xiangpeng Guo; Menghui Yin; Muqddas Tariq; Yiwei Lai; Shahzina Kanwal; Jiajian Zhou; Yuan Lv; Carlos Pulido-Quetglas; Xiwei Wang; Lu Ji; Muhammad J Khan; Xihua Zhu; Zhiwei Luo; Changwei Shao; Do-Hwan Lim; Xiao Liu; Nan Li; Wei Wang; Minghui He; Carl Ward; Tong Wang; Gong Zhang; Dongye Wang; Jianhua Yang; Yiwen Chen; Chaolin Zhang; Ralf Jauch; Yun-Gui Yang; Yangming Wang; Baoming Qin; Minna-Liisa Anko; Andrew P Hutchins; Hao Sun; Huating Wang; Xiang-Dong Fu; Biliang Zhang; Miguel A Esteban

doi:10.1038/nmeth.4595

Capturing the interactome of newly transcribed RNA

Xichen Bao
, Xiangpeng Guo
, Menghui Yin
, Muqddas Tariq
, Yiwei Lai
, Shahzina Kanwal
, Jiajian Zhou
, Yuan Lv
, Carlos Pulido-Quetglas
, Xiwei Wang
, Lu Ji
, Muhammad J Khan
, Xihua Zhu
, Zhiwei Luo
, Changwei Shao
, Do-Hwan Lim
, Xiao Liu
, Nan Li
, Wei Wang
, Minghui He

Carl Ward, Tong Wang, Gong Zhang, Dongye Wang, Jianhua Yang, Yiwen Chen, Chaolin Zhang, Ralf Jauch, Yun-Gui Yang, Yangming Wang, Baoming Qin, Minna-Liisa Anko, Andrew P Hutchins, Hao Sun, Huating Wang, Xiang-Dong Fu, Biliang Zhang, Miguel A Esteban

Biochemistry and Cell Biology

Research output: Contribution to journal › Article › Scientific › peer-review

187 Citations (Scopus)

Abstract

We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells. RICK will facilitate an in-depth interrogation of the total RNA-bound proteome in different cells and systems.

Original language	English
Pages (from-to)	213-220
Number of pages	8
Journal	Nature Methods
Volume	15
Issue number	3
DOIs	https://doi.org/10.1038/nmeth.4595
Publication status	Published - Mar 2018
MoE publication type	A1 Journal article-refereed

Keywords

Animals
Click Chemistry/methods
Embryonic Stem Cells/cytology
HeLa Cells
High-Throughput Nucleotide Sequencing/methods
Humans
Mass Spectrometry/methods
Mice
Protein Interaction Maps
Proteome/metabolism
RNA/genetics
RNA-Binding Proteins/genetics
Uridine/analogs & derivatives

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10.1038/nmeth.4595

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@article{4f25986c0f2f42cfaf2ba6ab08a39269,

title = "Capturing the interactome of newly transcribed RNA",

abstract = "We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells. RICK will facilitate an in-depth interrogation of the total RNA-bound proteome in different cells and systems.",

keywords = "Animals, Click Chemistry/methods, Embryonic Stem Cells/cytology, HeLa Cells, High-Throughput Nucleotide Sequencing/methods, Humans, Mass Spectrometry/methods, Mice, Protein Interaction Maps, Proteome/metabolism, RNA/genetics, RNA-Binding Proteins/genetics, Uridine/analogs \& derivatives",

author = "Xichen Bao and Xiangpeng Guo and Menghui Yin and Muqddas Tariq and Yiwei Lai and Shahzina Kanwal and Jiajian Zhou and Yuan Lv and Carlos Pulido-Quetglas and Xiwei Wang and Lu Ji and Khan, \{Muhammad J\} and Xihua Zhu and Zhiwei Luo and Changwei Shao and Do-Hwan Lim and Xiao Liu and Nan Li and Wei Wang and Minghui He and Carl Ward and Tong Wang and Gong Zhang and Dongye Wang and Jianhua Yang and Yiwen Chen and Chaolin Zhang and Ralf Jauch and Yun-Gui Yang and Yangming Wang and Baoming Qin and Minna-Liisa Anko and Hutchins, \{Andrew P\} and Hao Sun and Huating Wang and Xiang-Dong Fu and Biliang Zhang and Esteban, \{Miguel A\}",

year = "2018",

month = mar,

doi = "10.1038/nmeth.4595",

language = "English",

volume = "15",

pages = "213--220",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "3",

}

Bao, X, Guo, X, Yin, M, Tariq, M, Lai, Y, Kanwal, S, Zhou, J, Lv, Y, Pulido-Quetglas, C, Wang, X, Ji, L, Khan, MJ, Zhu, X, Luo, Z, Shao, C, Lim, D-H, Liu, X, Li, N, Wang, W, He, M, Ward, C, Wang, T, Zhang, G, Wang, D, Yang, J, Chen, Y, Zhang, C, Jauch, R, Yang, Y-G, Wang, Y, Qin, B, Anko, M-L, Hutchins, AP, Sun, H, Wang, H, Fu, X-D, Zhang, B & Esteban, MA 2018, 'Capturing the interactome of newly transcribed RNA', Nature Methods, vol. 15, no. 3, pp. 213-220. https://doi.org/10.1038/nmeth.4595

TY - JOUR

T1 - Capturing the interactome of newly transcribed RNA

AU - Bao, Xichen

AU - Guo, Xiangpeng

AU - Yin, Menghui

AU - Tariq, Muqddas

AU - Lai, Yiwei

AU - Kanwal, Shahzina

AU - Zhou, Jiajian

AU - Lv, Yuan

AU - Pulido-Quetglas, Carlos

AU - Wang, Xiwei

AU - Ji, Lu

AU - Khan, Muhammad J

AU - Zhu, Xihua

AU - Luo, Zhiwei

AU - Shao, Changwei

AU - Lim, Do-Hwan

AU - Liu, Xiao

AU - Li, Nan

AU - Wang, Wei

AU - He, Minghui

AU - Ward, Carl

AU - Wang, Tong

AU - Zhang, Gong

AU - Wang, Dongye

AU - Yang, Jianhua

AU - Chen, Yiwen

AU - Zhang, Chaolin

AU - Jauch, Ralf

AU - Yang, Yun-Gui

AU - Wang, Yangming

AU - Qin, Baoming

AU - Anko, Minna-Liisa

AU - Hutchins, Andrew P

AU - Sun, Hao

AU - Wang, Huating

AU - Fu, Xiang-Dong

AU - Zhang, Biliang

AU - Esteban, Miguel A

PY - 2018/3

Y1 - 2018/3

N2 - We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells. RICK will facilitate an in-depth interrogation of the total RNA-bound proteome in different cells and systems.

AB - We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells. RICK will facilitate an in-depth interrogation of the total RNA-bound proteome in different cells and systems.

KW - Animals

KW - Click Chemistry/methods

KW - Embryonic Stem Cells/cytology

KW - HeLa Cells

KW - High-Throughput Nucleotide Sequencing/methods

KW - Humans

KW - Mass Spectrometry/methods

KW - Mice

KW - Protein Interaction Maps

KW - Proteome/metabolism

KW - RNA/genetics

KW - RNA-Binding Proteins/genetics

KW - Uridine/analogs & derivatives

U2 - 10.1038/nmeth.4595

DO - 10.1038/nmeth.4595

M3 - Article

C2 - 29431736

SN - 1548-7091

VL - 15

SP - 213

EP - 220

JO - Nature Methods

JF - Nature Methods

IS - 3

ER -

Capturing the interactome of newly transcribed RNA

Abstract

Keywords

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