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.

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Acknowledgements

We thank all other members of the Laboratory of RNA, Chromatin, and Human Disease for their support, and we also thank R. Johnson (University of Bern, Switzerland), X. Zhang (Institute of Biophysics, Chinese Academy of Sciences, Beijing), L.-L. Chen (Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai), Y. Zhou (Wuhan University, Wuhan), M. Tortorella, and Q. Zheng (Guangzhou Institutes of Biomedicine and Health, Guangzhou), Y. Xu (Sun Yat-sen University, Guangzhou), and P. Liu (Anhui University, Hefei) for their expert comments and technical support. C.W. is supported by Zhujiang Talent-Overseas Postdoc Funding Grant, M.J.K. and S.K. are supported by CAS President's International Fellowships, and M.T. is supported by CAS-TWAS President's PhD Fellowship. This work was supported by the National Key Research and Development Program of China (2016YFA0100701 to X.B., 2016YFA0100102 to M.A.E., 2016YFA0100301 to B.Q., and 2017YFA0504400 to J.Y.), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502 to M.A.E.), the Pearl River Science and Technology Nova Program of Guangzhou (201610010107 to X.B., 201610010053 to W.W.), the Youth Innovation Promotion Association of the Chinese Academy of Sciences (2015294) to X.B.; the Cooperation Program of the Research Grants Council (RGC) of Hong Kong and the National Natural Science Foundation of China (NSFC; 81261160506 to M.A.E.); the NSFC (31371513 and 31671537 to M.A.E., 91440115 to B.Z., 81401909 to M.Y.), and 91440110 to J.Y., the General Research Funds from the RGC of Hong Kong (14116014 to H.W. 14113514 to H.S.), the Focused Innovations Scheme (Scheme B: 1907307 to H.S.), the RGC Collaborative Research Fund from RGC (C6015-14G to H.S. and H.W.), the Bureau of Science, Technology and Information of Guangzhou Municipality (2012J5100040 and 201508030027 to M.A.E.); the Natural Science Foundation of Guangdong Province (2014A030312001 to M.A.E., 2016A050503037 and 2015A030308007 to B.Q.); the Strategic Emerging Industry Key Technology Project of Guangdong Province (2012A080800006 to B.Z.), the Shenzhen Peacock Team Project (KQTD2015033117210153 to Nan L.); the Introduced Innovative R&D Team Program of Guangdong Province (201001Y0104789252 to B.Z.), the NIH Grant (R00CA175290) and the Cancer Prevention Research Institute of Texas First-Time Tenure-Track Faculty Recruitment Grant (RR140071) to Y.C. The Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine is supported by the Science and Technology Planning Project of Guangdong Province, China (2017B030314056).

Author information

Author notes

    • Xichen Bao
    • , Xiangpeng Guo
    •  & Menghui Yin

    These authors contributed equally to this work.

Affiliations

  1. 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.

    • Xichen Bao
    • , Xiangpeng Guo
    • , Muqddas Tariq
    • , Yiwei Lai
    • , Shahzina Kanwal
    • , Na Li
    • , Yuan Lv
    • , Xiwei Wang
    • , Muhammad J Khan
    • , Xihua Zhu
    • , Zhiwei Luo
    • , Carl Ward
    • , Dongye Wang
    • , Baoming Qin
    •  & Miguel A Esteban
  2. Laboratory of RNA, Chromatin, and Human Disease, Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

    • Xichen Bao
    • , Xiangpeng Guo
    • , Muqddas Tariq
    • , Yiwei Lai
    • , Shahzina Kanwal
    • , Na Li
    • , Yuan Lv
    • , Xiwei Wang
    • , Muhammad J Khan
    • , Xihua Zhu
    • , Zhiwei Luo
    • , Carl Ward
    • , Dongye Wang
    •  & Miguel A Esteban
  3. Laboratory of RNA Chemical Biology, State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

    • Menghui Yin
    •  & Biliang Zhang
  4. University of Chinese Academy of Sciences, Beijing, China.

    • Muqddas Tariq
    • , Yiwei Lai
    • , Yuan Lv
    •  & Zhiwei Luo
  5. 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.

    • Jiajian Zhou
    • , Lu Ji
    • , Hao Sun
    •  & Huating Wang
  6. Institute of Health Science, Anhui University, Hefei, China.

    • Na Li
  7. Department of Clinical Research, University of Bern, Bern, Switzerland.

    • Carlos Pulido-Quetglas
  8. Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Tarlai Kalan, Islamabad, Pakistan.

    • Muhammad J Khan
  9. Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.

    • Changwei Shao
    • , Do-Hwan Lim
    •  & Xiang-Dong Fu
  10. Department of Bioinformatics, GFK Biotech Inc., Shanghai, China.

    • Xiao Liu
  11. Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.

    • Nan Li
  12. Guangzhou RiboBio Co., Ltd., Guangzhou, China.

    • Wei Wang
  13. Forevergen Biosciences Center, Guangzhou, China.

    • Minghui He
  14. FitGene BioTechnology Co., Ltd., Guangzhou, China.

    • Yu-Lin Liu
  15. Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China.

    • Tong Wang
    •  & Gong Zhang
  16. Drug Discovery Pipeline Group, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

    • Dongye Wang
    •  & Ralf Jauch
  17. Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China.

    • Jianhua Yang
  18. Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

    • Yiwen Chen
  19. Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, New York, USA.

    • Chaolin Zhang
  20. 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.

    • Yun-Gui Yang
  21. Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.

    • Yangming Wang
  22. Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia.

    • Minna-Liisa Anko
  23. Department of Biology, Southern University of Science and Technology of China, Shenzhen, China.

    • Andrew P Hutchins

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Contributions

X.B. and M.A.E. conceived the idea, and X.G. contributed to the idea; X.B. and X.G. performed most of the experiments; M.Y. contributed to the experiments; M.T., Yiwei L., S.K., J.Z., Na L., Yuan L., C.P.-Q., X.W., L.J., M.J.K., X.Z., Z.L., C.S., D.-H.L., X.L., W.W., M.H., Y.-L.L., C.W., T.W., G.Z., D.W., J.Y., Y.C., C.Z., R.J., Y.-G.Y., Y.W., B.Q., M.-L.A., A.P.H., H.S., and X.-D.F. provided technical support, relevant advice, or performed computational analyses; Nan L., B.Q., H.W., and B.Z. provided infrastructural support; X.B., B.Z., and M.A.E. provided most of the financial support and supervised the project; X.B., X.G., and M.A.E. wrote the manuscript. X.B., B.Z., and M.A.E. approved the final version of the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Xichen Bao or Biliang Zhang or Miguel A Esteban.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–12, Supplementary Note 1 and Supplementary Table 7

  2. 2.

    Life Sciences Reporting Summary

  3. 3.

    Supplementary Protocol

    Capture of the newly transcribed RNA interactome using click chemistry

Excel files

  1. 1.

    Supplementary Table 1

    Distribution of different types of RNA captured by RICK

  2. 2.

    Supplementary Table 2

    CircRNAs identified by RICK and oligo(dT) capture

  3. 3.

    Supplementary Table 3

    Characterization of proteins isolated by RICK

  4. 4.

    Supplementary Table 4

    Analysis of RICK-identified RBPs

  5. 5.

    Supplementary Table 5

    Proteins identified by polyA-depleted RICK

  6. 6.

    Supplementary Table 6

    Short-labeling RICK time course and 16-hour RICK in mESCs

  7. 7.

    Supplementary Table 8

    List of primers and antibodies

  8. 8.

    Supplementary Table 9

    Statistics source data for Main Figures

  9. 9.

    Supplementary Table 10

    Statistics source data for Supplementary Figures