Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent manner
- Yi-Ying Chioua,1,
- Yanyan Yanga,1,
- Naim Rashidb,c,1,
- Rui Yea,
- Christopher P. Selbya, and
- Aziz Sancara,c,2
- aDepartment of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599;
- bDepartment of Biostatistics, University of North Carolina, Chapel Hill, NC 27599;
- cLineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
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Contributed by Aziz Sancar, August 17, 2016 (sent for review July 15, 2016; reviewed by Carl Hirschie Johnson and Andrew C. Liu)
Significance
The mammalian circadian clock is controlled by a transcription-translation feedback loop consisting of transcriptional activators circadian locomotor output cycles kaput (CLOCK)–brain and muscle Arnt-like protein-1 (BMAL1), which function as a complex at E/E'-box elements, and repressors Cryptochrome 1 (CRY1)/CRY2 and PER1/PER2. CRYs repress upon binding as CRY–CLOCK–BMAL1–E-box complexes. Period proteins (PERs) repress by removing the heterotrimeric complexes from the E-box. We report here that in the Cry1 promoter, the CRY1–CLOCK–BMAL1–E-box complex represses a transcriptional activator acting in cis, and removal of the heterotrimeric complex by PER2 de-represses the transcriptional activator. ChIP-seq and RNA-seq experiments identified other genes also de-repressed by PER2. These data clarify the role of PER2 and reveal the level of complexity in regulation of Cry1 and other circadian-controlled genes.
Abstract
The mammalian circadian clock is based on a transcription-translation feedback loop (TTFL) consolidated by secondary loops. In the primary TTFL, the circadian locomotor output cycles kaput (CLOCK)–brain and muscle Arnt-like protein-1 (BMAL1) heterodimer acts as the transcriptional activator, and Cryptochrome (CRY) and Period (PER) proteins function as repressors. PER represses by displacing CLOCK–BMAL1 from promoters in a CRY-dependent manner. Interestingly, genes with complex promoters may either be repressed or de-repressed by PER, depending on the particular promoter regulatory elements. Here, using mouse cell lines with defined knockout mutations in clock genes, RNA-seq, ChIP-seq, and reporter gene assays coupled with measurements of DNA–protein interactions in nuclear extracts, we elucidate the dual functions of PER as repressor and de-repressor in a context-dependent manner.
Footnotes
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↵1Y.-Y.C., Y.Y., and N.R. contributed equally to this work.
- ↵2To whom correspondence should be addressed. Email: aziz_sancar{at}med.unc.edu.
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Author contributions: Y.-Y.C., R.Y., and A.S. designed research; Y.-Y.C., Y.Y., and R.Y. performed research; Y.-Y.C., Y.Y., and N.R. analyzed data; and C.P.S. and A.S. wrote the paper.
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Reviewers: C.H.J., Vanderbilt University; and A.C.L., University of Memphis.
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The authors declare no conflict of interest.
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This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1612917113/-/DCSupplemental.
