Transcriptomics

Dataset Information

3

Non-circadian expression masking clock-driven weak transcription rhythms in U2OS cells


ABSTRACT: U2OS cells harbor a circadian clock but express only a few rhythmic genes in constant conditions. We identified 3040 binding sites of the circadian regulators BMAL1, CLOCK and CRY1 in the U2OS genome. Most binding sites even in promoters do not correlate with detectable rhythmic transcript levels. Luciferase fusions reveal that the circadian clock supports robust but low amplitude transcription rhythms of representative promoters. However, rhythmic transcription of these potentially clock-controlled genes is masked by non-circadian transcription that overwrites the weaker contribution of the clock in constant conditions. Our data suggest that U2OS cells harbor an intrinsically rather weak circadian oscillator. The oscillator has the potential to regulate a large number of genes. The contribution of circadian versus non-circadian transcription is dependent on the metabolic state of the cell and may determine the apparent complexity of the circadian transcriptome. Analysis of temporal expression profiles of 5708 expressed genes in synchronized U2OS cells. A 60k customized microarray was designed for 6356 genes, which corresponds to roughly one fourth of the human genome. 1373 genes were assigned to circadian regulator binding sites (CRBSs), 1503 genes were specifically selected in addition to a set of 3480 random genes. For each gene 10 independent probes in two microarray replicates were performed to increase reliability of the data.

ORGANISM(S): Homo sapiens  

SUBMITTER: Michael Brunner   Anton Shostak  Julia Hoffmann  Tamás Fischer  Felix Naef  Laura Symul 

PROVIDER: E-GEOD-57891 | ArrayExpress | 2014-05-23

SECONDARY ACCESSION(S): GSE57891PRJNA248370

REPOSITORIES: GEO, ArrayExpress

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