GEO DataSets

(Submitter supplied) In many bacteria, the base pairing between most small regulatory RNAs (sRNAs) and their targets is facilitated by the Hfq RNA chaperone. However, recent studies have shown FinO-domain proteins also bind sRNAs. To compare the contributions of Hfq and the FinO-domain ProQ protein in Escherichia coli, we carried out RIL-seq, which allows global identification of two RNAs bound to the same protein. We detected hundreds of RNA pairs on ProQ. more...

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL24570

56 Samples

Download data: BED, WIG

(Submitter supplied) Synthesis of flagella is very energy intensive and, while extensive transcriptional regulation has been described, little is known about the post-transcriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators; most base pairing with mRNAs to affect their stability and/or translation. Here we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor, sigma 28 in Escherichia coli. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24570

16 Samples

Download data: BIGWIG, WIG

(Submitter supplied) In many gram-negative and some gram-positive bacteria small regulatory RNAs (sRNAs) that bind the RNA chaperone Hfq have a pivotal role in modulating virulence, stress responses, metabolism, and biofilm formation. These sRNAs recognize transcripts through base-pairing, and sRNA-mRNA annealing consequently alters the translation and/or stability of transcripts leading to changes in gene expression. We have previously found that the highly conserved 3'-to-5' exoribonuclease polynucleotide phosphorylase (PNPase) has an indispensable role in paradoxically stabilizing Hfq-bound sRNAs and promoting their function in gene regulation in Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL15010

12 Samples

Download data: TXT, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24659 GPL26592

30 Samples

Download data: FA, GTF

(Submitter supplied) By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL24659

16 Samples

Download data: TXT

(Submitter supplied) By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

14 Samples

Download data: XLSX

(Submitter supplied) The Gram-negative pathogen Pasteurella multocida is responsible for many important animal diseases. While a number of P. multocida virulence factors have been identified, very little is known about how gene expression and protein production is regulated in this organism. One mechanism by which bacteria regulate transcript abundance and protein production is riboregulation, which involves the interaction of a small RNA (sRNA) with a target mRNA to alter transcript stability and/or translational efficiency. more...

Organism:

Pasteurella multocida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31945

9 Samples

Download data: CSV

(Submitter supplied) In pursuit of a biological role of Salmonella 3' UTR derived sRNA NarS, we sought to determine potential target mRNAs of NarS under anaerobic conditions. To this end, we compared gene expression in NarS-deficient and NarS overexpression (from plasmid pPL-NarS) strains following a 30-minute anaerobic shock by RNA-seq.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27045

2 Samples

Download data: TXT

(Submitter supplied) A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

9 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL33271 GPL23999

33 Samples

Download data: BW

(Submitter supplied) A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23999

12 Samples

Download data: BW

(Submitter supplied) A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL23999

12 Samples

Download data: BED, BW

(Submitter supplied) RNA-based regulation of gene expression is substantially contributing to the ability of bacteria to rapidly adapt to changing environmental conditions. This study employs RNAseq to define the transcriptome of Caulobacter in response to treatment with the DNA-crosslinking agent mitomycin C. We identify a small, regulatory RNA ChvR synthesized under the control of the conserved ChvIG two-component system which represses production of a TonB-dependent receptor, ChvT, in Caulobacter crescentus. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21317

6 Samples

Download data: WIG

(Submitter supplied) In this study binding sites for the RNA-binding protein ProQ was determined in Salmonella and Escherichia coli

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platforms:

GPL21117 GPL20056

10 Samples

Download data: WIG

(Submitter supplied) Hfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), the Escherichia coli mutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24570

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20051 GPL20056

42 Samples

Download data

(Submitter supplied) FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

24 Samples

Download data: CSV

(Submitter supplied) FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

6 Samples

Download data: CSV

(Submitter supplied) FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. more...

Organism:

Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20051

12 Samples

Download data: CSV

(Submitter supplied) Termination site sequencing (term-seq) (Dar et al., 2016) was used to map transcript 3' ends and potential processing sites in Campylobacter jejuni NCTC11168 wildtype and ribonuclease deletion strains.

Organism:

Campylobacter jejuni

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26884

10 Samples

Download data: WIG