Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Escherichia coli

SUBMITTER: Aswin Sai Narain Seshasayee

PROVIDER: E-MTAB-332 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of DNA relaxation in Dickeya dadantii wild type, fis and hns strains

Project description:We have analyzed the transcriptomes of Dickeya dadantii wild type, fis and hns strains in condition of DNA relaxation induced by novobiocin, a DNA gyrase inhibitor. For DNA relaxation novobiocin was added for 15 min to 100µg/ml final concentration to exponentially growing wild type, hns and fis strains (OD600= 0.2) grown in M63 medium supplemented by sucrose 0.2% (w/v). At this concentration, novobiocin has no impact on D. dadantii growth The micro-arrays used in this study were custom designed and produced by Roche NimbleGen, Inc. (Madison, WI) based on the annotated sequence of D. dadantii, available at Genbank accession number n° CP002038, which comprises 4597 CDS. The 4plex expression micro-arrays consist of 60-mer oligonucleotides, triplicated in three blocks on the array (5 oligonucleotides per CDS). For micro-array analyses, cDNA was synthesized, labeled and hybridized by Roche NimbleGen Inc.

2015-04-16 | E-MTAB-2597 | biostudies-arrayexpress

ChIP-seq investigation of H-NS of Escherichia coli grown in the presence and absence of an antibiotic "Bicyclomycin", a potential inhibitior of transcription termination factor rho.

Project description:We report that inhibition of rho by treatment with bicyclomycin, a potential inhibitor of rho affects H-NS binding to chromosome across most of the binding sites. For the current study, we have flag tagged H-NS by homologous recomination method. Cells were grown in the presence and absence of antibiotic bicylomyin. Chromatin immunoprecipitation was performed and anti flag antibody was used for immunoprecipitation. Immunoprecipitated samples both from BCM- and BCM + conditions were sequenced using HiSeq 1000 model. Input DNA was used as control for this experiment which was also sequenced. The 50-mer reads obtained were then mapped to Escherichia coli Mg1655 K-12 genome. Further analysis was carried out to calculate the ChIP signal score. We observed a drop in ChIP signal for bcm+ condition as compared to bcm-. ChIP-seq data generated by Hiseq 1000 model of samples with bcm+ and bcm- in biological duplicates along with Input DNA as control

2014-01-01 | E-GEOD-51582 | 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. One sample with four different treatments. Three biological replicates per sample. The Aerated 2 hour sample was set as the control condition for all samples.

2013-05-01 | E-GEOD-38661 | biostudies-arrayexpress

Chromatin immunoprecipitation of Escherichia coli HNS-FLAG pchABC mutants and LER-FLAG to determine Ler and H-NS distribution

Project description:Chromatin immunoprecipitation of EHEC to determine Ler and H-NS distribution

2010-02-28 | E-TABM-819 | biostudies-arrayexpress

Chromatin immunoprecipitation of Escherichia coli HNS-FLAG pchABC, pchBC and Ler mutants to determine Pch and H-NS distribution

Project description:Pch and H-NS distribution in EHEC O157 Sakai

2010-02-28 | E-TABM-818 | biostudies-arrayexpress

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

ChIP-chip analysis for H-NS binding sites in wild type and hhaydgT cells

Project description:Analysis of the distribution of the binding regions of the H-NS protein in E. coli W3110 and W3110hhaydgT mutant cells.

2013-04-04 | E-MEXP-3812 | biostudies-arrayexpress

Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA (ChIP-Seq)

Project description:Characterization of the activities of the transcription factors that AP3 and PI encode throughout flower development using perturbation and ChIPSeq assays in combination with a floral induction system (FIS) that allows a stage-specific analysis of flower development. Examination of genomic regions bound by fully functional AP3-GFP and PI-GFP proteins at approx floral stage 4-5 as compared to a negative control sample

2012-06-01 | E-GEOD-38358 | biostudies-arrayexpress

[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

Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUS (expression)

Project description:Characterization of the activities of the transcription factor that AG encodes throughout flower development using perturbation assays in combination with a floral induction system (FIS) that allows a stage-specific analysis of flower development. The series contains static perturbation experiments (null allele ag-1), and amiRNA knockdown experiments. Two conditions (i.e. perturbation experiments of ag-1 homozygous in the FIS vs ag-1 heterozygous in the FIS across three developmental stages. amiRNA knockdown experiments induced amiRNA expression vs. uninduced.

2013-07-01 | E-GEOD-44919 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data