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Series GSE35788 Query DataSets for GSE35788
Status Public on Dec 06, 2012
Title Genome-wide profiles of RNA polymerase II (Pol 2) DNA occupancy and the histone modifications H3K4me3 and H3K36me3 around the circadian cycle
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary To understand the transcriptional basis of circadian rhythms in mouse liver, we generated genome-wide profiles of RNA polymerase II (Pol 2) DNA occupancy and the histone modifications H3K4me3 and H3K36me3 around the circadian cycle. We found that Pol 2 occupancy at promoters and in gene bodies cycle in synchrony, suggesting that Pol 2 recruitment at promoters underlies circadian gene transcription. On average, Pol 2 occupancy precedes mRNA accumulation by about three hours. Promoters of transcribed genes have tri-methylated H3K4 residues even at their trough activity times, and the tri-methylation levels increase in phase with Pol 2 loading. In contrast, the tri-methylation of H3K36 residues lags transcription by three hours with amplitudes that are markedly shallower, indicating that this mark is less dynamic on the circadian time scale. The comparison of Pol 2 occupancy and mRNA accumulation revealed that both transcriptional and post-transcriptional regulatory mechanisms can account for diurnal mRNA profiles. Additional processed data and visualization tools are available at

Contributed by members of CycliX consortium (
Overall design 28 samples examinded, 7 Polr2b, 7 H3K4me3, 7 H3k36me3, 7 input samples.
Contributor(s) Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R, Martin O, Deplancke B, Delorenzi M, Desvergne B, Herr W, Rougemont J, Schibler U, Guex N, Hernandez N, Naef F
Citation(s) 23209382
Submission date Feb 13, 2012
Last update date May 15, 2019
Contact name Nouria Hernandez
Organization name UNIL
Department CIG
Lab Hernandez
Street address Dorigny
City Lausanne
State/province Vaud
ZIP/Postal code 1015
Country Switzerland
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (28)
GSM874950 Polr2b_ZT02
GSM874951 Polr2b_ZT06
GSM874952 Polr2b_ZT10
This SubSeries is part of SuperSeries:
GSE35790 Kinetic RNA polymerase II occupancy, associated histone marks, and mRNA accumulation reveal transcriptional and post-transcriptional mechanisms underlying circadian gene expression
SRA SRP010910
BioProject PRJNA155911

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Supplementary file Size Download File type/resource
GSE35788_RAW.tar 724.9 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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