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Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis

ABSTRACT: Fis and H-NS are two well-known NAPs in proteobacteria which play crucial role in both genome organization and gene regulation. However, the global effects of Fis and H-NS on gene expression remain unclear. Here, to decipher transcriptional regulatory roles of Fis and H-NS we have performed RNA-sequencing to compare gene expression between the wild-type E. coli and its knockout mutants for fis and hns. We integrated our RNA-seq results with publically available ChIP-seq data to define direct and indirect regulation by Fis and H-NS. The regulatory networks thus provide a comprehensive view of coordinated regulatory roles for these important nucleoid-associated proteins.

ORGANISM(S): Escherichia coli

PROVIDER: GSE123554 | GEO | 2018/12/11

REPOSITORIES: GEO

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[E-MTAB-332] H-NS and Fis binding to E. coli K12

Project description:Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear. Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA. ArrayExpress Release Date: 2010-07-29 Person Roles: submitter Person Last Name: Sai Narain Seshasayee Person First Name: Aswin Person Mid Initials: Person Email: aswin@ebi.ac.uk Person Phone: Person Address: Person Affiliation: EBI

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H-NS and Fis binding to E. coli K12

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TsrA regulates gene expression of horizontally acquired elements in Vibrio cholerae via both H-NS dependent and independent mechanisms [IPOD-HR]

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Transcription profiling of E. coli wild type and fis or hns transcription factor mutants in CSH50, LZ41 and LZ54 strains during different growth phases, with relaxation and hypernegative supercoiling and after norflaxacin treatment

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2013-01-30 | E-TABM-86 | biostudies-arrayexpress

Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis

Project description:Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis

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ChIP-seq of E. coli to identify H-NS and Fis binding at multiple time-points during growth in rich medium

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