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Science 338 (6105): 349-354

Copyright © 2012 by the American Association for the Advancement of Science

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

Nobuya Koike,1 Seung-Hee Yoo,1 Hung-Chung Huang,1 Vivek Kumar,1 Choogon Lee,2 Tae-Kyung Kim,1 Joseph S. Takahashi1,3,*

Abstract: The mammalian circadian clock involves a transcriptional feed back loop in which CLOCK and BMAL1 activate the Period and Cryptochrome genes, which then feedback and repress their own transcription. We have interrogated the transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver and find a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II (RNAPII) recruitment, RNA expression, and chromatin states. We find that the circadian transcriptional cycle of the clock consists of three distinct phases: a poised state, a coordinated de novo transcriptional activation state, and a repressed state. Only 22% of messenger RNA (mRNA) cycling genes are driven by de novo transcription, suggesting that both transcriptional and posttranscriptional mechanisms underlie the mammalian circadian clock. We also find that circadian modulation of RNAPII recruitment and chromatin remodeling occurs on a genome-wide scale far greater than that seen previously by gene expression profiling.

1 Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390–9111, USA.
2 Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA.
3 Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390–9111, USA.

* To whom correspondence should be addressed. E-mail: joseph.takahashi{at}

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