title: A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes.
abstract: BACKGROUND
  The circadian expression of the mammalian clock genes is based on transcriptional feedback loops. Two basic helix-loop-helix (bHLH) PAS (for Period-Arnt-Sim) domain-containing transcriptional activators, CLOCK and BMAL1, are known to regulate gene expression by interacting with a promoter element termed the E-box (CACGTG). The non-canonical E-boxes or E-box-like sequences have also been reported to be necessary for circadian oscillation.
  
  
  RESULTS
  We report a new cis-element required for cell-autonomous circadian transcription of clock genes. This new element consists of a canonical E-box or a non-canonical E-box and an E-box-like sequence in tandem with the latter with a short interval, 6 base pairs, between them. We demonstrate that both E-box or E-box-like sequences are needed to generate cell-autonomous oscillation. We also verify that the spacing nucleotides with constant length between these 2 E-elements are crucial for robust oscillation. Furthermore, by in silico analysis we conclude that several clock and clock-controlled genes possess a direct repeat of the E-box-like elements in their promoter region.
  
  
  CONCLUSIONS
  We propose a novel possible mechanism regulated by double E-box-like elements, not to a single E-box, for circadian transcriptional oscillation. The direct repeat of the E-box-like elements identified in this study is the minimal required element for the generation of cell-autonomous transcriptional oscillation of clock and clock-controlled genes.
authors.affiliation: Osaka Bioscience Institute, Suita, Osaka 565-0874, Japan. yasu_nakahata@yahoo.co.jp
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakahata
authors.forename: Mayumi
authors.initials: M
authors.lastname: Yoshida
authors.forename: Atsuko
authors.initials: A
authors.lastname: Takano
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Soma
authors.forename: Takuro
authors.initials: T
authors.lastname: Yamamoto
authors.forename: Akio
authors.initials: A
authors.lastname: Yasuda
authors.forename: Toru
authors.initials: T
authors.lastname: Nakatsu
authors.forename: Toru
authors.initials: T
authors.lastname: Takumi
mesh_terms: D056930:ARNTL Transcription Factors; D000818:Animals; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D056926:CLOCK Proteins; D002940:Circadian Rhythm / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D024721:E-Box Elements; D006801:Humans; D046911:Macromolecular Substances; D051379:Mice; D008957:Models, Genetic; D008958:Models, Molecular; D009154:Mutation; D041681:NIH 3T3 Cells; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D056950:Period Circadian Proteins; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D015533:Transcriptional Activation
chemical_list: D056930:ARNTL Transcription Factors; D051792:Basic Helix-Loop-Helix Proteins; D056926:CLOCK Proteins; D004247:DNA; D046911:Macromolecular Substances; D009687:Nuclear Proteins; D056950:Period Circadian Proteins; D015534:Trans-Activators; D014157:Transcription Factors; C538960:BMAL1 protein, human; C538961:Bmal1 protein, mouse; C421902:PER2 protein, human; C538943:CLOCK protein, human; C538944:Clock protein, mouse