Letter | Published:

ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm

Nature Genetics volume 49, pages 146151 (2017) | Download Citation

Abstract

It has been proposed that the CLOCK–ARNTL (BMAL1) complex drives circadian transcription of thousands of genes, including Per and Cry family genes that encode suppressors of CLOCK–ARNTL-dependent transcription1,2,3. However, recent studies demonstrated that 70–80% of circadian-oscillating mRNAs have no obvious rhythms in their de novo transcription4,5, indicating the potential importance of post-transcriptional regulation. Our CLOCK-ChIP-seq analysis identified rhythmic expression of adenosine deaminase, RNA-specific, B1 (Adarb1, also known as Adar2), an adenosine-to-inosine (A-to-I) RNA-editing enzyme. RNA-seq showed circadian rhythms of ADARB1-mediated A-to-I editing in a variety of transcripts. In Adarb1-knockout mice, rhythms of large populations of mRNA were attenuated, indicating a profound impact of ADARB1-mediated A-to-I editing on RNA rhythms. Furthermore, Adarb1-knockout mice exhibited short-period rhythms in locomotor activity and gene expression. These phenotypes were associated with abnormal accumulation of CRY2. The present study identifies A-to-I RNA editing as a key mechanism of post-transcriptional regulation in the circadian clockwork.

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Acknowledgements

We thank K. Yugi, Y. Sugiura and T. Kokaji for their help with metabolic analysis, and we thank T. Nakagawa for his help with RNA-seq data analysis. We also thank J. Nakano for critical comments on the manuscript. Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics. Adarb1−/−Gria2R/R mice were obtained from MMRRC 8U42OD010924-13. This work was partially supported by Grants-in-Aid for Scientific Research and Innovative Areas Genome Science from MEXT of Japan (to H.Y., W.I. and Y.F.), by the Japan Prize foundation (to H.Y.) and by Uchang Cho Institute of Science (to H.Y.). H.T. is supported by a JSPS research fellowship for young scientists.

Author information

Author notes

    • Haruka Ozaki

    Present address: Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, Saitama, Japan.

Affiliations

  1. Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan.

    • Hideki Terajima
    • , Hikari Yoshitane
    • , Shinya Kuroda
    • , Wataru Iwasaki
    •  & Yoshitaka Fukada
  2. Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

    • Haruka Ozaki
  3. Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

    • Yutaka Suzuki
  4. Department of Health Science, School of Pharmacy, Nihon University, Chiba, Japan.

    • Shigeki Shimba

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Contributions

H.T. performed almost all the experiments. H.T., H.O. and Y.S. conducted the transcriptome experiments and performed bioinformatic analysis. S.S. generated Arntl-knockout mice. S.K. supervised the KEGG pathway analysis and the metabolic experiments. H.Y., W.I. and Y.F. supervised the project. H.T., H.Y., H.O. and Y.F. co-wrote the manuscript. All authors discussed the results and contributed to the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Hikari Yoshitane or Yoshitaka Fukada.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–4 and Supplementary Table 4

Excel files

  1. 1.

    Supplementary Table 1

    List of the rhythmic genes that are common in four published papers4–7, and their CLOCK ChIP-seq scores modified from our previous study6

  2. 2.

    Supplementary Table 2

    Number of sequenced tags

  3. 3.

    Supplementary Table 3

    List of the rhythmic editing sites

  4. 4.

    Supplementary Table 5

    Gene expression profiles in RNA-seq of control and Adarb1-knockout mice

  5. 5.

    Supplementary Table 6

    List of primer sequences

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DOI

https://doi.org/10.1038/ng.3731