Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-Scale Mapping of Escherichia coli Ď54 Reveals Widespread, Conserved Intragenic Binding

ABSTRACT: Genome-Scale Mapping of Escherichia coli Ď54 Reveals Widespread, Conserved Intragenic Binding

PROVIDER: PRJEB9775 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR951783.fastq.gz	Fastqsanger.gz
	ERR951784.fastq.gz	Fastqsanger.gz
	ERR951785.fastq.gz	Fastqsanger.gz
	ERR951786.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Genome-Scale Mapping of Escherichia coli Ď54 Reveals Widespread, Conserved Intragenic Binding

Project description:Genome-Scale Mapping of Escherichia coli Ď54 Reveals Widespread, Conserved Intragenic Binding

| PRJEB9774 | ENA

Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding

Project description:We investigated the effect that intragenic s54 binding sites have on transcripton elongation. In an rpoN deletion we have over-expressed rpoN from a plasmid (with vector only contol) and then looked at changes in transcription elongation around intragenic s54 binding sites by RNA-seq. We are also looking at changes in transcription initiation/elongation at sites of sigma factor overlap.

2015-08-06 | E-MTAB-3699 | biostudies-arrayexpress

Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding.

Project description:Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5' UTRs.

| S-EPMC4591121 | biostudies-literature

Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding

Project description:We investigated the genome-wide binding sites for sigma54 and RNA polymerase in wild-type Escherichia coli MG1655.

2015-08-06 | E-MTAB-3697 | biostudies-arrayexpress

Rho directs widespread termination of intragenic and stable RNA transcription

Project description:The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found ~200 Rho-terminated loci that were divided evenly into two classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a novel set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a novel role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.

2009-06-23 | GSE16562 | GEO

Rho directs widespread termination of intragenic and stable RNA transcription

2010-05-18 | E-GEOD-16562 | biostudies-arrayexpress

High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program

Project description:High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program

| PRJNA240098 | ENA

Intragenic DNA inversions expand bacterial coding capacity

Project description:Bacteria can generate heterogeneity through phase variation, including enzyme-mediated inversion of specific intergenic regions of genomic DNA. We developed a computation tool that identifies invertible elements using long-read datasets, PhaVa. We identified over 300 ‘intragenic invertons,’ a new class of invertible elements entirely within genes, in both bacteria and archaea. In the gut commensal Bacteroides thetaiotaomicron, we experimentally characterized an intragenic inverton in the thiamine biosynthesis protein thiC. We used mass spectrometry in data-independent acquisition mode to identify and quantify B. theta proteins, including thiC inverton expression at the protein level.

2024-08-06 | PXD054577 | Pride

High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program

Project description:N6-methyladenosine (m6A) is the most ubiquitous mRNA base modification, but little is known about its precise location, temporal dynamics, and regulation. Here, we generated genomic maps of m6A sites in meiotic yeast transcripts at nearly single-nucleotide resolution, identifying 1,308 putatively methylated sites within 1,183 transcripts. We validated 8/8 methylation sites in different genes with direct genetic analysis, demonstrated that methylated sites are significantly conserved in a related species, and built a model that predicts methylated sites directly from sequence. Sites vary in their methylation profiles along a dense meiotic time-course, and are regulated both locally, via predictable methylatability of each site, and globally, through the core meiotic circuitry. The methyltransferase complex components localize to the yeast nucleolus, and this localization is essential for mRNA methylation. Our data illuminates a conserved, dynamically regulated methylation program in yeast meiosis, and provides an important resource for studying the function of this epitranscriptomic modification. Examination of m6A methylation under various conditions

2013-11-22 | E-GEOD-51583 | biostudies-arrayexpress

Widespread strain-specific distinctions in chromosomal binding dynamics of a highly conserved Escherichia coli transcription factor

Project description:Widespread strain-specific distinctions in chromosomal binding dynamics of a highly conserved Escherichia coli transcription factor

| PRJEB38405 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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