Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach.

Nucleic Acids Research
Sarath Chandra Janga, Bruno Contreras-Moreira

Abstract

In prokaryotes, regulation of gene expression is predominantly controlled at the level of transcription. Transcription in turn is mediated by a set of DNA-binding factors called transcription factors (TFs). In this study, we map the complete repertoire of ∼300 TFs of the bacterial model, Escherichia coli, onto gene expression data for a number of nonredundant experimental conditions and show that TFs are generally expressed at a lower level than other gene classes. We also demonstrate that different conditions harbor varying number of active TFs, with an average of about 15% of the total repertoire, with certain stress and drug-induced conditions exhibiting as high as one-third of the collection of TFs. Our results also show that activators are more frequently expressed than repressors, indicating that activation of promoters might be a more common phenomenon than repression in bacteria. Finally, to understand the association of TFs with different conditions and to elucidate their dynamic interplay with other TFs, we develop a network-based framework to identify TFs which act as markers, defined as those which are responsible for condition-specific transcriptional rewiring. This approach allowed us to pinpoint several marker TF...Continue Reading

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Jun 8, 2012·Molecular Ecology·Katy D HeathJohn R Stinchcombe
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Aug 24, 2018·Nucleic Acids Research·Ye GaoBernhard O Palsson

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