The Poly(C) Motif in the Proximal Promoter Region of the D Site-Binding Protein Gene ( Dbp) Drives Its High-Amplitude Oscillation

Mol Cell Biol. 2019 Jul 29;39(16):e00101-19. doi: 10.1128/MCB.00101-19. Print 2019 Aug 15.

Abstract

The D site-binding protein (Dbp) supports the rhythmic transcription of downstream genes, in part by displaying high-amplitude cycling of its own transcripts compared to other circadian-clock genes. However, the underlying mechanism remains elusive. Here, we demonstrated that the poly(C) motif within the Dbp proximal promoter, in addition to an E-box element, provoked transcriptional activation. Furthermore, we generated a cell line with poly(C) deleted to demonstrate the endogenous effect of the poly(C) motif within the Dbp promoter. We investigated whether RNA polymerase 2 (Pol2) recruitment on the Dbp promoter was decreased in the cell line with poly(C) deleted. Next, assay for transposase-accessible chromatin (ATAC)-quantitative PCR (qPCR) showed that the poly(C) motif induced greater chromatin accessibility within the region of the Dbp promoter. Finally, we determined that the oscillation amplitude of endogenous Dbp mRNA of the cell line with poly(C) deleted was decreased, which affected the oscillation of other clock genes that are controlled by Dbp Taken together, our results provide new insights into the function of the poly(C) motif as a novel cis-acting element of Dbp, along with its significance in the regulation of circadian rhythms.

Keywords: Dbp; circadian rhythm; mRNA oscillation; poly(C).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Animals
  • Chromatin / genetics
  • Circadian Clocks*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • Mice
  • NIH 3T3 Cells
  • Promoter Regions, Genetic
  • Protein Binding
  • RNA Polymerase II / metabolism*
  • Sequence Deletion
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • Chromatin
  • DNA-Binding Proteins
  • Dbp protein, mouse
  • Transcription Factors
  • RNA Polymerase II