Quantitative Genomic Analysis of RecA Protein Binding During DNA Double-Strand Break Repair Reveals RecBCD Action in vivo
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli
SUBMITTER: Charlotte Cockram
PROVIDER: E-GEOD-71249 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Study of the mechanisms of RecB mutant terminus DNA loss in Escherichia coli. FX158: WT MG1655 FX35: recB- FX37: ruvAB- FX51: matP- MIC18: recB- sbcD- sbcC- MIC20: recB- ruvAB- MIC24: matP- recB- MIC25: recA- recB- MIC31: sbcB- sbcD- MIC34: recA- recD- MIC40: linear chromosome MIC41: linear chromosome recB- MIC42: matP- ftsKC- MIC43: matP- ftsKC- recB- MIC48: recA- Cells were grown in M9 minimal medium supplemented with 0.4 % glucose to exponential phase (0.2 OD 650 nm). Chromosomal DNA was extracted using the Sigma GenElute bacterial genomic DNA kit. 5 μg of DNA were used to generate a genomic library according to Illumina's protocol. The libraries and the sequencing were performed by the High-throughput Sequencing facility of the I2BC (http://www.i2bc.paris-saclay.fr/spip.php?article399&lang=en, CNRS, Gif-sur-Yvette, France). Genomic DNA libraries were made with the ‘Nextera DNA library preparation kit’ (Illumina) following the manufacturer’s recommendations. Library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent technologies). Libraries were pooled in equimolar proportions. 75 bp single reads were generated on an Illumina MiSeq instrument, using a MiSeq Reagent kit V2 (500 cycles) (Illumina), with an expected depth of 217X. An in-lab written MATLAB-based script was used to perform marker frequency analysis. Reads were aligned on the Escherichia coli K12 MG1655 genome using BWA software. Data were normalized by dividing uniquely mapping sequence reads by the total number of reads. Enrichment of uniquely mapping sequence reads in 1 kb non-overlapping windows were calculated and plotted against the chromosomal coordinates.
2017-11-10 | E-MTAB-6122 | biostudies-arrayexpress
Project description:Bacteria are extremely versatile organisms which rapidly adapt to changing environments. When Escherichia coli cells switch from planktonic growth to biofilm, flagellum formation is turned off, and the production of fimbriae and extracellular polysaccharides is switched on. Here we show that BolA protein is a new bacterial transcription factor which modulates the switch from planktonic to sessile lifestyle. BolA negatively modulates flagella biosynthesis and thus swimming capacity. Furthermore, BolA overexpression favors biofilm formation and involvesinvolving fimbriae-like adhesins and curli production. Our results unraveled for the first time that BolA is a protein with high affinity to DNA, involved in the regulation of several genes of E. coli at a genome-wide scale level. Moreover, this observation further demonstrated that the most significant targets of this protein involved a complex network of genes encoding proteins extremely necessary in biofilm development processes. Herein we propose that BolA is a motile/adhesive transcriptional switch, specifically involved in the transition between the planktonic and the attachment stage of biofilm formation process. In the study presented here DNA enrichment was analyzed in 2 different strains, a strain containing bolA-3xflag-tag and a deletion mutant for this gene, which was used as the control sample.
2015-02-19 | E-GEOD-58623 | biostudies-arrayexpress
Project description:This dataset contains transcription profiles of TOP10 E.coli transformed with 85 rewired network plasmids first described in: Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840-5 (2008). The data are described and analysed in an accompanying paper Baumstark et al.,The propagation of perturbations in shuffled bacterial gene networks (Submitted, 2015). 260 raw data microarrays are provided in total, representing biological triplicates (a,b and c; independent colonies grown from the same transformation, under standard growth conditions; LB, 16h). This is done for each of 255 promoter-ORF constructs (e.g. appY-crp, etc.) and 5 control construct microarrays (empty plasmid; Co). Co controls are provided for comparison, to show the relative effect of the rewiring genetic perturbation. The final processed data compares the number of perturbed genes, comparing between the average expression values of each rewired construct and Co. Methods: The 85 rewiring plasmids (Isalan et al, 2008) were transformed into E. coli TOP10 cells and grown under standardised conditions: bacteria were freshly plated onto LB Agar plates (with 100 μg/ml Ampicillin and 50 μg/ml Streptomycin) and incubated overnight at 37oC to form colonies. Single colonies (<3 days old) were used to inoculate 2 ml of LB in 14 ml culture tubes, containing 100 μg/ml Ampicillin and 50 μg/ml Streptomycin. Constructs were grown for 16h at 37oC, at 220 rpm in an orbital shaker. 10 μg of extracted total bacterial RNA (integrity number > 7.0) was used with Affymetrix GeneChip E. coli Genome 2.0 Arrays. Key to names: RAW DATA samples 1-260 _Co_1a.CEL = Control Co, colony a _Co_1b.CEL = Control Co, colony b etc. appY_O_30a.CEL = appY-promoter only, colony a appY_O_30b.CEL = appY-promoter only, colony b etc. appY_crp_34a.CEL = rewired construct, appY-promoter expressing crp ORF, colony a appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony b appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony c etc. PROCESSED DATA sample 261: probe_set_expression_value_norm_all - normalised data for all samples, for all E. coli K12 genes sample 262: probe_set_expression_value_norm_MG1655 - normalised data for all samples, for E. coli MG1655 subset of genes
2015-12-14 | E-MTAB-3233 | biostudies-arrayexpress
Project description:Using a highly efficient and strand-specific RNA-seq method combined with a highly accurate and robust algorithm and tool we developed, TruHMM for assembling full-length transcriptomes, to profile the transcriptome of E.coli K12 under different culture conditions and growth phases, we showed that the dynamic transcriptome structures appears to be culture condition and growth phases dependent. mRNA profiles of E.coli K12 cultured under different treaments including LB (OD=0.87), Heatshock (15min, 30min, 60min), and MOPS-P(0h,2h,4h).
2013-06-21 | E-GEOD-48151 | biostudies-arrayexpress
Project description:Most E. coli sRNAs interact with their mRNA targets through simultaneous binding to the Hfq chaperon. In this experiment we cross-linked RNA to proteins in-vivo then did Hfq IP followed by ligation of bound RNAs and sequencing to identify sRNA-mRNA interactions. We termed the method RIL-seq for RNA Interactions by Ligation - sequencing.
2016-07-30 | E-MTAB-3910 | biostudies-arrayexpress
Project description:In this experiment, we carried out a global analysis of specific RNAs that are bound to the RelA protein. CLIP-Seq experiment was carried out with E. coli RelA wild type and RelA::C289Y mutant strains. Libraries were prepared and high throughput sequencing was done.
2021-09-16 | E-MTAB-10884 | biostudies-arrayexpress
Project description:Here we show using RNA-seq that cleavage by RNase E direct entry pervades in both the degradation and processing of RNA. We also give further evidence that direct entry is facilitated by cooperative interaction with segments in addition to the ones in which cleavage occurs. RNA seq profiles were compared between a temperature-sensitive mutant of rne and its congenic wild-type incubated at a non-permissive temperature. RNA seq profiles were also compared between samples before and after incubation with a 5'-sensing mutant of RNase E in vitro.
2014-06-10 | E-GEOD-58285 | biostudies-arrayexpress
Project description:UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additionally crosslinked Hfq in non-pathogenic E. coli K12 str. MG1655 grown in LE media. Hfq-RNA complexes were purified and trimmed using RNase A/T1. RNA fragments were isolated and converted to cDNA, PCR amplified and sequenced using Illumina Solexa GAxII and HiSeq2000 platforms. His-FLAG tagged Hfq and untagged controls were cultured to an OD of 0.8 and crosslinked with UV-C. Five replicates of tagged EHEC Hfq and 2 replicates of untagged Hfq were crosslinked. We have additionally crosslinked 2 replicates each of E. coli K12 tagged and untagged Hfq.
2014-05-22 | E-GEOD-46118 | biostudies-arrayexpress
Project description:ChIP-seq to identify sigma38 binding sites in wild-type and delta ssrS (6S RNA knockout) strains of E. Coli K-12 MG1655, during stationary phase ChIP-seq using antibody against sigma38 in wild-type and ssrS deletion strain. Two replicates for wild type and one replicate for ssrS deletion.
2016-06-10 | E-GEOD-74836 | biostudies-arrayexpress
Project description:In the present study, we investigated the transcriptional expression patterns of the model strain E. coli exposed to titanium dioxide nanoparticles (NP-TiO2), under dark conditions by using a microarray. Expression profiles were compared to unexposed E.coli and ratio of expression were analysed. Cell exposure to NP-TiO2 was conducted in 10 mM NaCl, E. coli bacterial suspension and NP-TiO2 stock suspension (or mQ water for the control) were added to the NaCl solution to obtain final concentrations of 10E7 cells/ml and 100 mg/l of TiO2 nanoparticles. The flasks were then incubated at 20M-BM-0C on a dark rotary shaker for 5 h. Exposed NP-TiO2: 4 biological replicats. Control: 4 biological replicats.
2014-09-08 | E-GEOD-55972 | biostudies-arrayexpress