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Dynamic transcriptome structure of E. coli K-12 MG1655 across growth

ABSTRACT: High-resolution transcriptional profiling of E. coli across nine timepoints of growth in rich media (LB). Samples collected from lag phase to stationary phase of growth. High-resolution tiling array to detect conditional operon isoforms. Custom Agilent array designed to detect condition-specific transcriptional isoforms. Array designed for E coli K12 MG1655 genome. Tiled using 23bp sliding window. Includes >10,000 probes surrounding predicted operon break sites at 6 bp resolution. Nine growth time points in the experiment. Two-color arrays. Each time point compared to mid-exponential phase of growth.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Aaron Brooks

PROVIDER: E-GEOD-55879 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A system-level model for the microbial regulatory genome.

Brooks Aaron N AN Reiss David J DJ Allard Antoine A Wu Wei-Ju WJ Salvanha Diego M DM Plaisier Christopher L CL Chandrasekaran Sriram S Pan Min M Kaur Amardeep A Baliga Nitin S NS

Molecular systems biology 20140715

Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional infl ...[more]

PMID: 25028489

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Dynamic transcriptome structure of E. coli K-12 MG1655 across growth

Project description:High-resolution transcriptional profiling of E. coli across nine timepoints of growth in rich media (LB). Samples collected from lag phase to stationary phase of growth. High-resolution tiling array to detect conditional operon isoforms. Custom Agilent array designed to detect condition-specific transcriptional isoforms. Array designed for E coli K12 MG1655 genome. Tiled using 23bp sliding window. Includes >10,000 probes surrounding predicted operon break sites at 6 bp resolution.

2014-07-22 | GSE55879 | GEO

RNA sequencing based analysis of the bacterial transcriptome

Project description:To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture. E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media (carbon, nitrogen, or phosphate limited) and the total transcriptome of log and stationary phase samples was sequenced.

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Hi-C study of the E. coli MG1655 chromosome

Project description:We performed Hi-C analysis of Escherichia coli MG1655 cells in exponential and stationary growth phase. We could detect long-range interactions predominantly in the Ori domain of the chromosome. Interestingly, the use of a new type of control revealed that these interactions are mostly crosslinking independent. 6 samples from exponential phase growth in M9 medium; 6 samples from stationary phase growth in M9 medium; for each growth condition, 3 samples were with crosslinking and 3 samples were without.

2015-09-01 | E-GEOD-61658 | biostudies-arrayexpress

Unexpected complexity of the Escherichia coli K-12 transcriptome architecture revealed by single nucleotide resolution RNA sequencing

Project description:To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture. E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media and the total transcriptome of log and stationary phase samples was sequenced.

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Project description:Streptococcus pyogenes chromosomal island M1 (SpyCIM1) integrates by site-specific recombination into the 5’ end of DNA mismatch repair (MMR) gene mutL in strain SF370SmR, blocking transcription of it and the downstream operon genes. During exponential growth, SpyCIM1 excises from the chromosome and replicates as an episome, restoring mutL transcription. This process is reversed in stationary phase with SpyCIM1 re-integrating into mutL, returning the cells to a mutator phenotype. Here we show that elimination of SpyCIM1 relieves this mutator phenotype. The downstream MMR operon genes, multidrug efflux pump lmrP, Holliday junction resolution helicase ruvA, and DNA base excision repair glycosylase tag, are also restored to constitutive expression by elimination of SpyCIM1. The presence of SpyCIM1 alters global transcription patterns in SF370SmR. RNA sequencing (RNA-Seq) demonstrated that loss of SpyCIM1 in the SpyCIM1 deletion mutant, CEM1∆4, impacted the expression of many genes both in early exponential phase, when the SpyCIM1 is episomal, as well as at the onset of stationary phase, when SpyCIM1 has reintegrated into mutL. Among these changes, the up regulation of the genes for the antiphagocytic M protein (emm1), streptolysin O (slo), capsule operon (hasABC), and streptococcal pyrogenic exotoxin (speB), are particularly notable. The expression pattern of the DNA mismatch repair (MMR) operon confirmed our earlier observations that these genes are transcribed in early exponential phase but silenced as stationary phase is approached. The direct role of SpyCIM1 in causing the mutator phenotype is confirmed by these studies, and its influence upon the biology of S. pyogenes was found to impact multiple genes in addition to the MMR operon. We suggest that such chromosomal islands are a remarkable evolutionary adaptation to promote the survival of its S. pyogenes host cell in changing environments.

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Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (3C-Seq)

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