1. Molecular Medicine Laboratories, Institute for Drug Discovery Research, Yamanouchi Pharmaceutical Company, Ltd, 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
2. Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan
3. Department of Anatomy and Neurobiology, Kinki University School of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan
4. Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan

Correspondence to: Hiroki R. Ueda^1,2Yasufumi Shigeyoshi³ Correspondence and requests for materials should be addressed to H.R.U. (e-mail: Email: hiro@m.u-tokyo.ac.jp) or to Y.S. (e-mail: Email: shigey@med.kindai.ac.jp).

Abstract

Mammalian circadian clocks consist of complex integrated feedback loops^{1, 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.