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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: PRJEB9774 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR951779.fastq.gz	Fastqsanger.gz
	ERR951780.fastq.gz	Fastqsanger.gz
	ERR951781.fastq.gz	Fastqsanger.gz
	ERR951782.fastq.gz	Fastqsanger.gz

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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

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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.

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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.

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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.

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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.

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