Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

ABSTRACT: The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers. However, the specificity of the response across stimuli and cell types, and the roles of non-coding RNAs are not well understood. Using a large collection of densely-sampled time series expression data we have examined the induction of the immediate-early response in unparalleled detail, across cell types and stimuli. We exploit cap analysis of gene expression (CAGE) time series datasets to directly measure promoter activities over time. Using a novel analysis method for time series data we identify transcripts with expression patterns that closely resemble the dynamics of known immediate-early genes (IEGs) and this enables a comprehensive comparative study

SUBMITTER: Aitken S 

PROVIDER: S-EPMC4401570 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature