Letter | Published:

Transcriptional interference by antisense RNA is required for circadian clock function

Nature volume 514, pages 650653 (30 October 2014) | Download Citation

Abstract

Eukaryotic circadian oscillators consist of negative feedback loops that generate endogenous rhythmicities1. Natural antisense RNAs are found in a wide range of eukaryotic organisms2,3,4,5. Nevertheless, the physiological importance and mode of action of most antisense RNAs are not clear6,7,8,9. frequency (frq) encodes a component of the Neurospora core circadian negative feedback loop, which was thought to generate sustained rhythmicity10. Transcription of qrf, the long non-coding frq antisense RNA, is induced by light, and its level oscillates in antiphase to frq sense RNA3. Here we show that qrf transcription is regulated by both light-dependent and light-independent mechanisms. Light-dependent qrf transcription represses frq expression and regulates clock resetting. Light-independent qrf expression, on the other hand, is required for circadian rhythmicity. frq transcription also inhibits qrf expression and drives the antiphasic rhythm of qrf transcripts. The mutual inhibition of frq and qrf transcription thus forms a double negative feedback loop that is interlocked with the core feedback loop. Genetic and mathematical modelling analyses indicate that such an arrangement is required for robust and sustained circadian rhythmicity. Moreover, our results suggest that antisense transcription inhibits sense expression by mediating chromatin modifications and premature termination of transcription. Taken together, our results establish antisense transcription as an essential feature in a circadian system and shed light on the importance and mechanism of antisense action.

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Accessions

Primary accessions

Sequence Read Archive

Data deposits

RNA-Seq data are available at the Sequence Read Archive under accession number SRP030415.

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Acknowledgements

We thank J. Cha, Y. Dang and H. Yuan for technical assistance, and B. Li for critical comments. Supported by grants from the National Institutes of Health to Y.L. (GM068496, GM062591) and N.L.G. (GM081597), the Welch Foundation (I-1560) to Y.L., the Cancer Prevention Research Institute of Texas (RP101496) to Z. X., and the Biotechnology and Biological Sciences Research Council (BBS/S/C2005/13012) to S.R.A. and S.K.C.

Author information

Affiliations

  1. Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA

    • Zhihong Xue
    • , Qiaohong Ye
    •  & Yi Liu
  2. Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK

    • Simon R. Anson
    •  & Susan K. Crosthwaite
  3. Department of Clinical Sciences, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA

    • Jichen Yang
    •  & Guanghua Xiao
  4. Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA

    • David Kowbel
    •  & N. Louise Glass

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Contributions

Z.X., S.R.A., S.K.C. and Y.L. designed experiments. Z.X., S.R.A., J.Y. and D.K. performed experiments. Q.Y. provided technical support. Y.L., Z.X., S.R.A., N.L.G. and S.K.C. analysed data. Y.L., Z.X. and S.K.C. wrote the paper.

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The authors declare no competing financial interests.

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Correspondence to Yi Liu.

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https://doi.org/10.1038/nature13671

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