Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation

*Department of Neurobiology and Physiology, and
^‡Howard Hughes Medical Institute, Northwestern University, Evanston, IL 60208;
^§Department of Regulatory Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037;
^¶Department of Biochemistry, The Scripps Research Institute, Jupiter, FL 33458;
**Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121;
^††School of Kinesiology, University of Illinois, Chicago, IL 60608;
^‡‡Department of Cancer Biology, Cleveland Clinic Foundation, Cleveland, OH 44195; and
^§§Department of Physiology, University of Kentucky, Lexington, KY 40536

Contributed by Joseph S. Takahashi, December 30, 2006 (received for review December 8, 2006)

Abstract

Circadian rhythms of cell and organismal physiology are controlled by an autoregulatory transcription-translation feedback loop that regulates the expression of rhythmic genes in a tissue-specific manner. Recent studies have suggested that components of the circadian pacemaker, such as the Clock and Per2 gene products, regulate a wide variety of processes, including obesity, sensitization to cocaine, cancer susceptibility, and morbidity to chemotherapeutic agents. To identify a more complete cohort of genes that are transcriptionally regulated by CLOCK and/or circadian rhythms, we used a DNA array interrogating the mouse protein-encoding transcriptome to measure gene expression in liver and skeletal muscle from WT and Clock mutant mice. In WT tissue, we found that a large percentage of expressed genes were transcription factors that were rhythmic in either muscle or liver, but not in both, suggesting that tissue-specific output of the pacemaker is regulated in part by a transcriptional cascade. In comparing tissues from WT and Clock mutant mice, we found that the Clock mutation affects the expression of many genes that are rhythmic in WT tissue, but also profoundly affects many nonrhythmic genes. In both liver and skeletal muscle, a significant number of CLOCK-regulated genes were associated with the cell cycle and cell proliferation. To determine whether the observed patterns in cell-cycle gene expression in Clock mutants resulted in functional dysregulation, we compared proliferation rates of fibroblasts derived from WT or Clock mutant embryos and found that the Clock mutation significantly inhibits cell growth and proliferation.

Footnotes

^¶¶To whom correspondence should be addressed. E-mail: j-takahashi{at}northwestern.edu
Author contributions: B.H.M. and E.L.M. contributed equally to this work; B.H.M., E.L.M., K.A.E., J.B.H., and J.S.T. designed research; B.H.M., E.L.M., S.P., K.R.H., J.Z., J.L.A., M.P.A., and J.R.W. performed research; B.H.M., E.L.M., J.R.W., J.B.H., and J.S.T. analyzed data; and B.H.M., E.L.M., J.B.H., and J.S.T. wrote the paper.
↵ ^†Present address: The Scripps Research Institute, Jupiter, FL 33458.
↵ ^‖Present address: Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104.
The authors declare no conflict of interest.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE3751).
This article contains supporting information online at www.pnas.org/cgi/content/full/0611724104/DC1.
Abbreviations:

CT,

circadian time;

DD,

constant darkness;

LD,

light/dark;

MEF,

mouse embryonic fibroblast;

MMCβ,

multiple measures correct β;

SCN,

suprachiasmatic nucleus.
Freely available online through the PNAS open access option.