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A transcription factor response element for gene expression during circadian night

Author

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  • Hiroki R. Ueda

    (Yamanouchi Pharmaceutical Company, Ltd
    The University of Tokyo)

  • Wenbin Chen

    (Yamanouchi Pharmaceutical Company, Ltd)

  • Akihito Adachi

    (Kinki University School of Medicine)

  • Hisanori Wakamatsu

    (Yamanouchi Pharmaceutical Company, Ltd)

  • Satoko Hayashi

    (Yamanouchi Pharmaceutical Company, Ltd)

  • Tomohiro Takasugi

    (Yamanouchi Pharmaceutical Company, Ltd)

  • Mamoru Nagano

    (Kinki University School of Medicine)

  • Ken-ichi Nakahama

    (Kinki University School of Medicine)

  • Yutaka Suzuki

    (The University of Tokyo)

  • Sumio Sugano

    (The University of Tokyo)

  • Masamitsu Iino

    (The University of Tokyo)

  • Yasufumi Shigeyoshi

    (Kinki University School of Medicine)

  • Seiichi Hashimoto

    (Yamanouchi Pharmaceutical Company, Ltd)

Abstract

Mammalian circadian clocks consist of complex integrated feedback loops1,2,3,4,5,6,7,8,9,10 that cannot be elucidated without comprehensive measurement of system dynamics and determination of network structures11. To dissect such a complicated system, we took a systems-biological approach based on genomic, molecular and cell biological techniques. We profiled suprachiasmatic nuclei and liver genome-wide expression patterns under light/dark cycles and constant darkness. We determined transcription start sites of human orthologues for newly identified cycling genes and then performed bioinformatical searches for relationships between time-of-day specific expression and transcription factor response elements around transcription start sites. Here we demonstrate the role of the Rev-ErbA/ROR response element in gene expression during circadian night, which is in phase with Bmal1 and in antiphase to Per2 oscillations. This role was verified using an in vitro validation system, in which cultured fibroblasts transiently transfected with clock-controlled reporter vectors exhibited robust circadian bioluminescence12.

Suggested Citation

  • Hiroki R. Ueda & Wenbin Chen & Akihito Adachi & Hisanori Wakamatsu & Satoko Hayashi & Tomohiro Takasugi & Mamoru Nagano & Ken-ichi Nakahama & Yutaka Suzuki & Sumio Sugano & Masamitsu Iino & Yasufumi S, 2002. "A transcription factor response element for gene expression during circadian night," Nature, Nature, vol. 418(6897), pages 534-539, August.
    • Handle: RePEc:nat:nature:v:418:y:2002:i:6897:d:10.1038_nature00906
    DOI: 10.1038/nature00906
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    Citations

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    Cited by:

    1. Cheng-Kang Chiang & Neel Mehta & Abhilasha Patel & Peng Zhang & Zhibin Ning & Janice Mayne & Warren Y L Sun & Hai-Ying M Cheng & Daniel Figeys, 2014. "The Proteomic Landscape of the Suprachiasmatic Nucleus Clock Reveals Large-Scale Coordination of Key Biological Processes," PLOS Genetics, Public Library of Science, vol. 10(10), pages 1-15, October.
    2. Li, Ying & Liu, Zengrong, 2015. "Dynamical mechanism of Bmal1/Rev-erbĪ± loop in circadian clock," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 430(C), pages 126-135.
    3. Naveenarani Murugan & Ravinder Kumar & Shashi Kant Pandey & Pooja Dhansu & Mahadevaiah Chennappa & Saranya Nallusamy & Hemaprabha Govindakurup & Appunu Chinnaswamy, 2023. "In Silico Dissection of Regulatory Regions of PHT Genes from Saccharum spp. Hybrid and Sorghum bicolor and Expression Analysis of PHT Promoters under Osmotic Stress Conditions in Tobacco," Sustainability, MDPI, vol. 15(2), pages 1-17, January.
    4. Yasuko O. Abe & Hikari Yoshitane & Dae Wook Kim & Satoshi Kawakami & Michinori Koebis & Kazuki Nakao & Atsu Aiba & Jae Kyoung Kim & Yoshitaka Fukada, 2022. "Rhythmic transcription of Bmal1 stabilizes the circadian timekeeping system in mammals," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. Alan L Hutchison & Mark Maienschein-Cline & Andrew H Chiang & S M Ali Tabei & Herman Gudjonson & Neil Bahroos & Ravi Allada & Aaron R Dinner, 2015. "Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data," PLOS Computational Biology, Public Library of Science, vol. 11(3), pages 1-29, March.
    6. Andrey A Ptitsyn & Sanjin Zvonic & Steven A Conrad & L Keith Scott & Randall L Mynatt & Jeffrey M Gimble, 2006. "Circadian Clocks Are Resounding in Peripheral Tissues," PLOS Computational Biology, Public Library of Science, vol. 2(3), pages 1-10, March.

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