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

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

PROVIDER: PRJNA509204 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8309840_1.fastq.gz	Fastqsanger.gz
	SRR8309840_2.fastq.gz	Fastqsanger.gz
	SRR8309841_1.fastq.gz	Fastqsanger.gz
	SRR8309841_2.fastq.gz	Fastqsanger.gz
	SRR8309842_1.fastq.gz	Fastqsanger.gz

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

Project description: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.

2018-12-11 | GSE123554 | GEO

[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

2011-02-05 | GSE24991 | GEO

H-NS and Fis binding to E. coli K12

Project description:H-NS and Fis binding to E. coli K12

| PRJEB2225 | ENA

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

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.<br><br>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.

2010-09-01 | E-MTAB-332 | biostudies-arrayexpress

Fis occupancy along the Salmonella enterica serovar Typhimurium SL1344 fis::3XFlag strain grown in different aeration regimes.

Project description:The regulatory role of the Fis protein in fis and in the transcription of several gene regions during mid-exponential and late-stationary phase, and during different growth aeration regimes, has been investigated. Studies were done during those two growth phases and in aerated and non-aerated (microaerobic) conditions, to measure Fis enrichment and binding peaks in strategic gene regions by genome-wide microarray analysis ChIP-chip. This research investigation points to central roles for SPI-1, SPI-2, DNA gyrase and topoisomerase I, the elements of the stringent response, and the regulatory function of Fis-binding patterns, in setting and re-setting the activity of the fis gene and other involved promoters as a function of the growth conditions and aeration regimes experienced by Salmonella.

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Project description:Elucidating regulatory relationships between transcription factors (TFs) and target genes is fundamental to understanding how cells control their identity and behavior. To overcome the limited scope and scalability of experimental methods in mapping this control, computational GRN reconstruction methods have been developed to infer relationships from transcriptomic data. We developed a new computational GRN reconstruction tool called Epoch, which takes advantage of single-cell RNA sequencing to address a number of shortcomings of existing tools including low precision, low sensitivity, and the limited ability to describe network topology changes over time. We used Epoch to identify the dynamic networks and key transcriptional regulators underpinning directed differentiation of mouse embryonic stem cells, and further demonstrate that modulating signaling pathways drives topological network changes that shape cell fate potential. By integrating signaling pathways with GRN structures, we traced how Wnt activation and PI3K suppression govern mesoderm and endoderm specification, respectively.

2022-01-27 | GSE177051 | GEO

WT (Fis+) strain

Project description:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Keywords: time course

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Fis KO strain

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