GEO DataSets

(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) 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) Bacterial small regulatory RNAs (sRNAs) regulate gene expression by base-pairing to their target mRNAs. In Escherichia coli and many other bacteria, this process is dependent on the RNA chaperone Hfq, which binds sRNAs and mRNAs on different faces. YhbS (renamed here as HqbA), a putative Gcn5-related N-acetyltransferase (GNAT), was identified as a novel silencer of sRNA signaling in a genomic library screen. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18956

24 Samples

Download data: 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 alpha-proteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24555

2 Samples

Download data: XLSX

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

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21016 GPL28356

10 Samples

Download data

(Submitter supplied) In this study we determined the target spectrum of C. crescentus sRNA R0199 via pulse-expression followed by RNA-sequencing.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28356

6 Samples

Download data: XLSX

(Submitter supplied) In this study we used RNA co-immunoprecipitation followed by RNA-sequencing to identify Hfq-binding RNAs in C. crescentus.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21016

4 Samples

Download data: XLSX

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

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: GPR, GTF, TXT

(Submitter supplied) 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. more...

Organism:

Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17026 GPL17024 GPL17025

11 Samples

Download data: GTF

(Submitter supplied) Transcript abundance in Escherichia coli O157:H7 was determined in the presence or absence of pulsed expression of the small RNA, AsxR.

Organism:

Escherichia coli; Escherichia coli O157:H7

Type:

Expression profiling by array

Platform:

GPL3051

1 Sample

Download data: GPR, TXT

(Submitter supplied) The control of amino acid synthesis and transport in bacteria has been well-investigated at the transcriptional level. The discovery of a small Hfq-dependent regulatory RNA, GcvB, added another layer of gene expression control at the post-transcriptional level. GcvB RNA has been shown to directly regulate multiple ABC transporters for amino acids in E. coli and Salmonella using a highly conserved G/U-rich domain, R1. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platform:

GPL11416

8 Samples

Download data: TXT

(Submitter supplied) Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we performed MAPS with CyaR sRNA.

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19168

2 Samples

Download data: TXT

(Submitter supplied) Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we perform MAPS with RprA sRNA.

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL19168

2 Samples

Download data: TXT

(Submitter supplied) We report the identification of new noncoding RNAs in Brucella suis 1330 and that are associated to the chaperone protein Hfq

Organism:

Brucella suis 1330

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20974

2 Samples

Download data: GR

(Submitter supplied) Ribosome biogenesis is a complex and intricate process involving multiple factors. A plethora of auxiliary proteins assist the correct assembly of rRNA and ribosomal proteins into mature ribosomes. Defects in this process cause dysfunctional ribosomes which may alter protein synthesis and impair cell fitness. Despite its importance, yet we are lacking mechanistic details of ribosome biogenesis. Here we show that the widely-conserved RNA chaperone Hfq, which is an important post-transcriptional regulator in sRNA-mRNA basepairing in Escherichia coli, plays a critical role in rRNA processing and consequently ribosome assembly. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL14548

4 Samples

Download data: TAB