Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14946-51. doi: 10.1073/pnas.0802636105. Epub 2008 Sep 24.


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 ( 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • ARNTL Transcription Factors
  • Animals
  • Base Sequence
  • Basic Helix-Loop-Helix Transcription Factors / metabolism
  • Basic-Leucine Zipper Transcription Factors
  • Binding, Competitive
  • CLOCK Proteins
  • Circadian Rhythm / genetics*
  • DNA-Binding Proteins / metabolism
  • Databases, Genetic
  • Enhancer Elements, Genetic*
  • Gene Expression Regulation*
  • Humans
  • Mice
  • Promoter Regions, Genetic*
  • Sequence Analysis, DNA
  • Trans-Activators / metabolism
  • Transcription Factors / metabolism*


  • ARNTL Transcription Factors
  • ARNTL protein, human
  • Arntl protein, mouse
  • Basic Helix-Loop-Helix Transcription Factors
  • Basic-Leucine Zipper Transcription Factors
  • DBP protein, human
  • DNA-Binding Proteins
  • NFIL3 protein, human
  • Trans-Activators
  • Transcription Factors
  • CLOCK Proteins
  • CLOCK protein, human
  • Clock protein, mouse