Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli
| Autor: | Zhe Sun, Yan Ning Zhou, Cedric Cagliero, William F. Heinz, Jerome Izard, Ding Jun Jin, Thomas D. Schneider, Chen Y |
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| Rok vydání: | 2019 |
| Předmět: |
DNA
Bacterial Salinity Transcription Genetic Sequence analysis Information Theory Sigma Factor Biology Potassium Chloride Transcriptome 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Transcription (biology) Osmotic Pressure RNA polymerase Genetics Escherichia coli Promoter Regions Genetic Gene 030304 developmental biology 0303 health sciences Models Genetic Gene regulation Chromatin and Epigenetics Promoter DNA-Directed RNA Polymerases Gene Expression Regulation Bacterial Cell biology Culture Media genomic DNA enzymes and coenzymes (carbohydrates) chemistry bacteria DNA Intergenic 030217 neurology & neurosurgery DNA |
| Zdroj: | Nucleic acids research. 47(8) |
| ISSN: | 1362-4962 |
| Popis: | RNA polymerase (RNAP), the transcription machinery, shows dynamic binding across the genomic DNA under different growth conditions. The genomic features that selectively redistribute the limited RNAP molecules to dictate genome-wide transcription in response to environmental cues remain largely unknown. We chose the bacterial osmotic stress response model to determine genomic features that direct genome-wide redistribution of RNAP during the stress. Genomic mapping of RNAP and transcriptome profiles corresponding to the different temporal states after salt shock were determined. We found rapid redistribution of RNAP across the genome, primarily at σ70 promoters. Three subsets of genes exhibiting differential salt sensitivities were identified. Sequence analysis using an information-theory based σ70 model indicates that the intergenic regions of salt-responsive genes are enriched with a higher density of σ70 promoter-like sites than those of salt-sensitive genes. In addition, the density of promoter-like sites has a positive linear correlation with RNAP binding at different salt concentrations. The RNAP binding contributed by the non-initiating promoter-like sites is important for gene transcription at high salt concentration. Our study demonstrates that hyperdensity of σ70 promoter-like sites in the intergenic regions of salt-responsive genes drives the RNAP redistribution for reprograming the transcriptome to counter osmotic stress. |
| Databáze: | OpenAIRE |
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