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

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:

• circadian rhythm
• Dbp
• mRNA oscillation
• poly(C)

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at https://doi.org/10.1128/MCB.00101-19.

ACKNOWLEDGMENTS

This work was supported by the Bio and Medical Technology Development Program (2017M3C7A1023478) and a grant (2019R1A2C2009440) from the National Research Foundation (NRF), funded by the Korean government (MSIT); the Cooperative Research Program for Agriculture Science and Technology Development (project no. PJ01324801) of the Rural Development Administration; and BK21 Plus, funded by the Ministry of Education, Republic of Korea (10Z20130012243).

P.K.K., H.-M.K., S.W.K., and B.K. conducted and analyzed the experiments; H.Y. and H.-O.K. analyzed the lumicycle data; T.-Y.R. and K.-T.K. designed the experiments; P.K.K. and K.-T.K. wrote the paper.

We declare no conflict of interest.