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N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation

Nature Chemical Biology volume 15, pages 88–94 (2019)Cite this article

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Abstract

N6-Methyladenosine (m6A) RNA modification is present in messenger RNAs (mRNA), ribosomal RNAs (rRNA), and spliceosomal RNAs (snRNA) in humans. Although mRNA m6A modifications have been extensively studied and shown to play critical roles in many cellular processes, the identity of m6A methyltransferases for rRNAs and the function of rRNA m6A modifications are unknown. Here we report a new m6A methyltransferase, ZCCHC4, which primarily methylates human 28S rRNA and also interacts with a subset of mRNAs. ZCCHC4 knockout eliminates m6A4220 modification in 28S rRNA, reduces global translation, and inhibits cell proliferation. We also find that ZCCHC4 protein is overexpressed in hepatocellular carcinoma tumors, and ZCCHC4 knockout significantly reduces tumor size in a xenograft mouse model. Our results highlight the functional significance of an rRNA m6A modification in translation and in tumor biology.

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Fig. 1: ZCCHC4 methylates 28S rRNA in vitro.
Fig. 2: ZCCHC4 catalyzes 28S rRNA methylation in cells.
Fig. 3: ZCCHC4 activity affects translation.
Fig. 4: ZCCHC4 expression in tumor tissues and its effects on xenograft tumor progression.

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  • 08 February 2019

    In the version of this article originally published, the references were incorrectly re-ordered during production. The hyphen in “N6-methyladenosine” in the title was also superscript. The errors have been corrected in the HTML and PDF versions of the paper.

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Acknowledgements

We thank X. Wang, L. Hu, H. Shi, F. Liu, and J. Wei from C.H.’s laboratory for discussions and for sharing experiments materials. We thank J. Tauler for editing the manuscript. This work was supported by the National Institutes of Health grants HG008935 (to C.H.) and GM113194 (to T.P. and C.H.). C.H. is an investigator of the Howard Hughes Medical Institute (HHMI). This work also supported by National Natural Science Foundation of China (81602513; to J.C.) and funds from Fudan University, H.M. is supported by the Postdoctoral International Exchange Program of the China Postdoctoral Council (CPC). X.W. is supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under Award Number 1K01 DK111764.

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Author notes

  1. These authors contributed equally: Honghui Ma, Xiaoyun Wang, Jiabin Cai.

Authors and Affiliations

  1. Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China

    Honghui Ma, Ruitu Lv, Hao Chen, Yujiang Geno Shi, Fei Lan & Yang Shi

  2. Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA

    Honghui Ma, Qing Dai, Kai Chen, Zhike Lu & Chuan He

  3. Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA

    Honghui Ma, Qing Dai, Kai Chen, Zhike Lu & Chuan He

  4. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA

    Xiaoyun Wang, Tao Pan & Chuan He

  5. Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China

    Jiabin Cai & Jia Fan

  6. Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France

    S. Kundhavai Natchiar & Bruno P. Klaholz

  7. Endocrinology Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    Yujiang Geno Shi

  8. Department of Cell Biology, Harvard Medical School, Boston, MA, USA

    Yang Shi

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Contributions

H.M., T.P., Y.S. and C.H. designed the experiments. H.M. purified the recombinant ZCCHC4 protein, established the ZCCHC4 knockout stable cell lines, and carried out the in vitro and in vivo enzyme activity experiments and rescue experiments. X.W. performed polysome profile sequencing and reporter assays. J.C. performed WB and IHC in liver cancer samples and tumor growth assay in nude mice. Q.D. and K.C. assisted with enzyme activity experiments. R.L. and Z.L. helped with PAR-CLIP analysis. H.C. and Y.G.S. helped measure in vivo enzyme activity. F.L. helped design the experiments. J.F. helped prepare patient samples and analyze data. S.K.N. and B.P.K. helped with cryo-EM analysis of the m6A4220 modification site. H.M., X.W., T.P., Y.S. and C.H. wrote the manuscript.

Corresponding authors

Correspondence to Tao Pan, Yang Shi or Chuan He.

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Competing interests

Y.S. is a co-founder of Constellation Pharmaceuticals, Inc., and Athelas Therapeutics. C.H. is a scientific founder of Accent Therapeutics, Inc. and a member of its scientific advisory board.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10

Reporting Summary

Supplementary Dataset 1

PAR-CLIP showing ZCCHC4-bound RNAs in cells

Supplementary Dataset 2

ZCCHC4 KO affects translation

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Ma, H., Wang, X., Cai, J. et al. N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol 15, 88–94 (2019). https://doi.org/10.1038/s41589-018-0184-3

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