Genomics

Dataset Information

316

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals [ChIP-seq]


ABSTRACT: 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. Examination of 9 transcriptional regulators, 2 RNAPII and 6 histone modifications every 4hr during the circadian cycle in mouse liver

ORGANISM(S): Mus musculus  

SUBMITTER: Hung-Chung Huang   Nobuya Koike  Choogon Lee  Seung-Hee Yoo  Joseph S Takahashi  Tae-Kyung Kim  Vivek Kumar 

PROVIDER: E-GEOD-39977 | ArrayExpress | 2012-08-31

SECONDARY ACCESSION(S): SRP014752GSE39977PRJNA172197

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Transcriptional architecture and chromatin landscape of the core circadian clock in mammals.

Koike Nobuya N   Yoo Seung-Hee SH   Huang Hung-Chung HC   Kumar Vivek V   Lee Choogon C   Kim Tae-Kyung TK   Takahashi Joseph S JS  

Science (New York, N.Y.) 20120830 6105


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  ...[more]

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