title: Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock.
abstract: Mammalian circadian clocks consist of regulatory loops mediated by Clock/Bmal1-binding elements, DBP/E4BP4 binding elements, and RevErbA/ROR binding elements. As a step toward system-level understanding of the dynamic transcriptional regulation of the oscillator, we constructed and used a mammalian promoter/enhancer database (http://promoter.cdb.riken.jp/) with computational models of the Clock/Bmal1-binding elements, DBP/E4BP4 binding elements, and RevErbA/ROR binding elements to predict new targets of the clock and subsequently validated these targets at the level of the cell and organism. We further demonstrated the predictive nature of these models by generating and testing synthetic regulatory elements that do not occur in nature and showed that these elements produced high-amplitude circadian gene regulation. Biochemical experiments to characterize these synthetic elements revealed the importance of the affinity balance between transactivators and transrepressors in generating high-amplitude circadian transcriptional output. These results highlight the power of comparative genomics approaches for system-level identification and knowledge-based design of dynamic regulatory circuits.
authors.affiliation: Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Kumaki
authors.forename: Maki
authors.initials: M
authors.lastname: Ukai-Tadenuma
authors.forename: Ken-ichiro D
authors.initials: KD
authors.lastname: Uno
authors.forename: Junko
authors.initials: J
authors.lastname: Nishio
authors.forename: Koh-hei
authors.initials: KH
authors.lastname: Masumoto
authors.forename: Mamoru
authors.initials: M
authors.lastname: Nagano
authors.forename: Takashi
authors.initials: T
authors.lastname: Komori
authors.forename: Yasufumi
authors.initials: Y
authors.lastname: Shigeyoshi
authors.forename: John B
authors.initials: JB
authors.lastname: Hogenesch
authors.forename: Hiroki R
authors.initials: HR
authors.lastname: Ueda
mesh_terms: D056930:ARNTL Transcription Factors; D000818:Animals; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000378:metabolism; D050976:Basic-Leucine Zipper Transcription Factors; D001667:Binding, Competitive; D056926:CLOCK Proteins; D002940:Circadian Rhythm / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000378:metabolism; D030541:Databases, Genetic; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D015534:Trans-Activators / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D056930:ARNTL Transcription Factors; D051792:Basic Helix-Loop-Helix Proteins; D050976:Basic-Leucine Zipper Transcription Factors; D056926:CLOCK Proteins; D004268:DNA-Binding Proteins; D015534:Trans-Activators; D014157:Transcription Factors; C538960:BMAL1 protein, human; C538961:Bmal1 protein, mouse; C063898:DBP protein, human; C497440:NFIL3 protein, human; C538943:CLOCK protein, human; C538944:Clock protein, mouse