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Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks

Nature Cell Biology volume 10, pages 1154–1163 (2008)Cite this article

Abstract

Mammalian circadian clocks consist of complex regulatory loops mediated through—at least—morning, daytime and night-time DNA elements. To prove the transcriptional logic of mammalian clocks, we developed an in cellulo mammalian cell-culture system that allowed us to design and implement artificial transcriptional circuits. Here we show that morning activation and night-time repression can yield the transcriptional output during the daytime, and similarly that daytime activation and morning repression can yield night-time transcriptional output. We also observed that the diverse transcriptional outputs of other phases can be generated through the expression of simple combinations of transcriptional activators and repressors. These results reveal design principles not only for understanding the continuous transcriptional outputs observed in vivo but also for the logical construction of artificial promoters working at novel phases. Logical synthesis of artificial circuits, with an identified structure and observed dynamics, provides an alternative strategy applicable to the investigation of complex biological systems.

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Figure 1: Using an in cellulo mammalian cell-culture system for the physical simulation of natural transcriptional circuits.
Figure 2: Proof-by-synthesis of daytime and night-time transcriptional regulations.
Figure 3: Synthesis of various output phases from three basic circadian phases in artificial transcriptional circuits.
Figure 4: Transcriptional mechanisms to generate various output phases.
Figure 5: Transcriptional logic underlying mammalian circadian clocks.

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Acknowledgements

This research was supported by an intramural Grant-in-Aid from CDB (H.R.U.), the Uehara Memorial Foundation (H.R.U.) and KAKENHI (Grant-in-Aid for Scientific Research) on Priority Areas 'Systems Genomics' from the Ministry of Education, Culture, Sports, Science and Technology of Japan (H.R.U.). We thank Hideki Ukai for critical discussion, Rikuhiro G. Yamada and Tetsuya J. Kobayashi for programming the real-time bioluminescence data analysis, Yuichi Kumaki for the Promoter Database, and Erik A. Kuld, Douglas Sipp and Michael Royle for critical reading of the manuscript.

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  1. Takeya Kasukawa: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Hyogo, Japan

    Maki Ukai-Tadenuma & Hiroki R. Ueda

  2. Functional Genomics Unit, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Hyogo, Japan

    Takeya Kasukawa & Hiroki R. Ueda

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Contributions

H.R.U. developed the concept of the proof-by-synthesis of the transcriptional logic underlying mammalian circadian clocks. M.U. constructed all materials used in this work and performed the real-time luminescence assays. T.K. developed the data analysis methods for the in cellulo and in silico data, and conducted these analyses. All the authors discussed the results and commented on the manuscript text.

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Correspondence to Hiroki R. Ueda.

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Ukai-Tadenuma, M., Kasukawa, T. & Ueda, H. Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks. Nat Cell Biol 10, 1154–1163 (2008). https://doi.org/10.1038/ncb1775

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