Capturing the interactome of newly transcribed RNA

Xichen Bao; Xiangpeng Guo; Menghui Yin; Muqddas Tariq; Yiwei Lai; Shahzina Kanwal; Jiajian Zhou; Na Li; 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; Yu Lin Liu; 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, Na Li, 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 WangMinghui He, Yu Lin Liu, 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

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

109 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 - 1 Mar 2018

Keywords

interactome
RNA binding protein
labelling
proteomic analysis
proteomics

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10.1038/nmeth.4595

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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 = "interactome, RNA binding protein, labelling, proteomic analysis, proteomics",

author = "Xichen Bao and Xiangpeng Guo and Menghui Yin and Muqddas Tariq and Yiwei Lai and Shahzina Kanwal and Jiajian Zhou and Na Li 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 Lim, {Do Hwan} and Xiao Liu and Nan Li and Wei Wang and Minghui He and Liu, {Yu Lin} 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 Yang, {Yun Gui} and Yangming Wang and Baoming Qin and Anko, {Minna Liisa} and Hutchins, {Andrew P.} and Hao Sun and Huating Wang and Fu, {Xiang Dong} and Biliang Zhang and Esteban, {Miguel A.}",

year = "2018",

month = mar,

day = "1",

doi = "10.1038/nmeth.4595",

language = "English",

volume = "15",

pages = "213--220",

journal = "Nature Methods",

issn = "1548-7091",

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Bao, X, Guo, X, Yin, M, Tariq, M, Lai, Y, Kanwal, S, Zhou, J, Li, N, Lv, Y, Pulido-Quetglas, C, Wang, X, Ji, L, Khan, MJ, Zhu, X, Luo, Z, Shao, C, Lim, DH, Liu, X, Li, N, Wang, W, He, M, Liu, YL, Ward, C, Wang, T, Zhang, G, Wang, D, Yang, J, Chen, Y, Zhang, C, Jauch, R, Yang, YG, Wang, Y, Qin, B, Anko, ML, Hutchins, AP, Sun, H, Wang, H, Fu, XD, 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 - Li, Na

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 - Liu, Yu Lin

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 - 2018/3/1

Y1 - 2018/3/1

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 - interactome

KW - RNA binding protein

KW - labelling

KW - proteomic analysis

KW - proteomics

UR - http://www.scopus.com/inward/record.url?scp=85042756849&partnerID=8YFLogxK

U2 - 10.1038/nmeth.4595

DO - 10.1038/nmeth.4595

M3 - Article

AN - SCOPUS:85042756849

VL - 15

SP - 213

EP - 220

JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

IS - 3

ER -

Capturing the interactome of newly transcribed RNA

Abstract

Keywords

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