Linking Core Promoter Classes to Circadian Transcription

PLoS Genet. 2016 Aug 9;12(8):e1006231. doi: 10.1371/journal.pgen.1006231. eCollection 2016 Aug.


Circadian rhythms in transcription are generated by rhythmic abundances and DNA binding activities of transcription factors. Propagation of rhythms to transcriptional initiation involves the core promoter, its chromatin state, and the basal transcription machinery. Here, I characterize core promoters and chromatin states of genes transcribed in a circadian manner in mouse liver and in Drosophila. It is shown that the core promoter is a critical determinant of circadian mRNA expression in both species. A distinct core promoter class, strong circadian promoters (SCPs), is identified in mouse liver but not Drosophila. SCPs are defined by specific core promoter features, and are shown to drive circadian transcriptional activities with both high averages and high amplitudes. Data analysis and mathematical modeling further provided evidence for rhythmic regulation of both polymerase II recruitment and pause release at SCPs. The analysis provides a comprehensive and systematic view of core promoters and their link to circadian mRNA expression in mouse and Drosophila, and thus reveals a crucial role for the core promoter in regulated, dynamic transcription.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / genetics
  • Circadian Rhythm / genetics*
  • Drosophila melanogaster / genetics
  • Gene Expression Regulation
  • Liver / metabolism
  • Mice
  • Models, Theoretical
  • Period Circadian Proteins / biosynthesis
  • Period Circadian Proteins / genetics*
  • Promoter Regions, Genetic*
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / genetics
  • TATA Box
  • Transcription, Genetic*


  • Chromatin
  • Period Circadian Proteins
  • RNA, Messenger

Grant support

Funding from the German Ministry of Science and Education (BMBF), FKZ 0315899, is hereby acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.