Capturing the interactome of newly transcribed RNA.

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

doi:10.1038/nmeth.4595

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Journal article

Capturing the interactome of newly transcribed RNA.

Bao X Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Guo X Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Yin M Laboratory of RNA Chemical Biology, State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Tariq M Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Lai Y Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Kanwal S Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Zhou J Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
Li N Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Lv Y Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Pulido-Quetglas C Department of Clinical Research, University of Bern, Bern, Switzerland.
Wang X Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Ji L Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
Khan MJ Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Zhu X Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Luo Z Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Shao C Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.
Lim DH Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.
Liu X Department of Bioinformatics, GFK Biotech Inc., Shanghai, China.
Li N Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.
Wang W Guangzhou RiboBio Co., Ltd., Guangzhou, China.
He M Forevergen Biosciences Center, Guangzhou, China.
Liu YL FitGene BioTechnology Co., Ltd., Guangzhou, China.
Ward C Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Wang T Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China.
Zhang G Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China.
Wang D Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Yang J Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China.
Chen Y Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Zhang C Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, New York, USA.
Jauch R Drug Discovery Pipeline Group, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Yang YG Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Center for Excellence in Molecular Cell Science, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Wang Y Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.
Qin B Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Anko ML Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia.
Hutchins AP Department of Biology, Southern University of Science and Technology of China, Shenzhen, China.
Sun H Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
Wang H Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
Fu XD Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.
Zhang B Laboratory of RNA Chemical Biology, State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Esteban MA Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.

2018-02-13

Published in:

Nature methods. - 2018

High-Throughput Nucleotide Sequencing

English 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.

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English

Open access status

green

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DOI 10.1038/nmeth.4595
PMID 29431736

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https://sonar.ch/global/documents/185279

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Journal article

Capturing the interactome of newly transcribed RNA.

Animals

Click Chemistry

Embryonic Stem Cells

HeLa Cells

High-Throughput Nucleotide Sequencing

Humans

Mass Spectrometry

Mice

Protein Interaction Maps

Proteome

RNA

RNA-Binding Proteins

Uridine

Statistics