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Series GSE36874 Query DataSets for GSE36874
Status Public on Nov 10, 2012
Title Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control. Based predominantly on the transcription feedback loops important for core circadian timekeeping, it is commonly assumed that this widespread mRNA cycling reflects circadian transcriptional cycling. To address this issue, we directly measured dynamic changes in mouse liver transcription using Nascent-Seq. Many genes are rhythmically transcribed over the 24h day, which include precursors of several non-coding RNAs as well as the expected set of core clock genes. Surprisingly however, nascent RNA rhythms overlap poorly with mRNA abundance rhythms assayed by RNA-seq. This is because most mouse liver genes with rhythmic mRNA expression manifest poor transcriptional rhythms, indicating a prominent role of post-transcriptional regulation in setting mRNA cycling amplitude. To gain further insight into circadian transcriptional regulation, we also characterized the rhythmic transcription of liver genes targeted by the transcription factors CLOCK and BMAL1; they directly target other core clock genes and sit at the top of the molecular circadian clock hierarchy in mammals. CLK:BMAL1 rhythmically bind at the same discrete phase of the circadian cycle to all target genes, which not surprisingly have a much higher percentage of rhythmic transcription than the genome as a whole. However, there is a surprisingly heterogeneous set of cycling transcription phases of direct target genes, which even include core clock genes. This indicates a disconnect between rhythmic DNA binding and the peak of transcription, which is likely due to other transcription factors that collaborate with CLK:BMAL1. In summary, the application of Nascent-Seq to a mammalian tissue provides surprising insights into the rhythmic control of gene expression and should have broad applications beyond the analysis of circadian rhythms.
 
Overall design CLK and BMAL1 DNA binding profile in the mouse liver at ZT8, sequenced along an Input sample using GAII (ChIP-Seq)
Supplementary file ChIPSeq_Mouse_Liver_Processed_data_Table1.txt represents annotated CLK and BMAL1 peaks.
 
Contributor(s) Menet JS, Rodriguez J, Rosbash M
Citation(s) 23150795
Submission date Mar 28, 2012
Last update date May 15, 2019
Contact name Jerome S Menet
E-mail(s) menet@bio.tamu.edu
Organization name Texas A&M University
Department Dept of Biology
Street address 301 Old Main Drive, Building 1530, ILSB
City College Station
State/province TX
ZIP/Postal code 77843
Country USA
 
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (3)
GSM904671 ChIP-Seq_Mouse_Liver_ZT8_CLK
GSM904672 ChIP-Seq_Mouse_Liver_ZT8_BMAL1
GSM904673 ChIP-Seq_Mouse_Liver_ZT8_Input
This SubSeries is part of SuperSeries:
GSE36916 Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation
Relations
SRA SRP011982
BioProject PRJNA157205

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE36874_ChIPSeq_Mouse_Liver_Processed_data_Table1.txt.gz 321.4 Kb (ftp)(http) TXT
GSE36874_RAW.tar 60.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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