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Status |
Public on Aug 31, 2012 |
Title |
Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals [RNA-seq] |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
The mammalian circadian clock involves a transcriptional feedback 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. Interestingly only 22% of mRNA cycling genes are driven by de novo transcription, suggesting that both transcriptional and post-transcriptional 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.
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Overall design |
Examination of whole transcriptome every 4hr during the circadian cycle in mouse liver
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Contributor(s) |
Koike N, Yoo S, Huang H, Kumar V, Lee C, Kim T, Takahashi JS |
Citation(s) |
22936566 |
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Submission date |
Aug 08, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Joseph S Takahashi |
E-mail(s) |
[email protected]
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Phone |
214-648-1876
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Organization name |
University of Texas Southwestern Medical Center
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Department |
HHMI, Neuroscience
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Lab |
Joseph S. Takahashi
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Street address |
5323 Harry Hines Blvd., NA4.118
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City |
Dallas |
State/province |
TX |
ZIP/Postal code |
75390-9111 |
Country |
USA |
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Platforms (1) |
GPL14602 |
AB SOLiD 4 System (Mus musculus) |
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Samples (12)
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GSM982826 |
Sample 1_whole transcriptome (RNA-seq) |
GSM982827 |
Sample 2_whole transcriptome (RNA-seq) |
GSM982828 |
Sample 3_whole transcriptome (RNA-seq) |
GSM982829 |
Sample 4_whole transcriptome (RNA-seq) |
GSM982830 |
Sample 5_whole transcriptome (RNA-seq) |
GSM982831 |
Sample 6_whole transcriptome (RNA-seq) |
GSM982832 |
Sample 7_whole transcriptome (RNA-seq) |
GSM982833 |
Sample 8_whole transcriptome (RNA-seq) |
GSM982834 |
Sample 9_whole transcriptome (RNA-seq) |
GSM982835 |
Sample 10_whole transcriptome (RNA-seq) |
GSM982836 |
Sample 11_whole transcriptome (RNA-seq) |
GSM982837 |
Sample 12_whole transcriptome (RNA-seq) |
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This SubSeries is part of SuperSeries: |
GSE39860 |
Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals |
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Relations |
BioProject |
PRJNA172198 |
SRA |
SRP014751 |