Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation (Q34122762)

31 July 2017

title

Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation (English)

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31 July 2017

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Ivana Bilusic

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31 July 2017

Niko Popitsch

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31 July 2017

Philipp Rescheneder

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31 July 2017

Renée Schroeder

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31 July 2017

Meghan Lybecker

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31 July 2017

publication date

12 June 2014

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31 July 2017

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31 July 2017

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31 July 2017

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31 July 2017

page(s)

641-654

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The double-stranded transcriptome of Escherichia coli

31 July 2017

cites work

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28 July 2018

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Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system

28 July 2018

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Regulatory RNAs and target mRNA decay in prokaryotes.

28 July 2018

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28 July 2018

Cycling of RNAs on Hfq.

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Association of RNAs with Bacillus subtilis Hfq.

28 July 2018

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Bacterial small RNA-based negative regulation: Hfq and its accomplices

28 July 2018

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28 July 2018

A decade of riboswitches

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Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY.

28 July 2018

1 reference

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Genome-wide antisense transcription drives mRNA processing in bacteria

28 July 2018

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Regulation by small RNAs in bacteria: expanding frontiers

28 July 2018

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Genome-wide detection of novel regulatory RNAs in E. coli

28 July 2018

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cis-antisense RNA, another level of gene regulation in bacteria.

28 July 2018

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RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Bacterial antisense RNAs: how many are there, and what are they doing?

28 July 2018

1 reference

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Widespread antisense transcription in Escherichia coli.

28 July 2018

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BigWig and BigBed: enabling browsing of large distributed datasets

28 July 2018

1 reference

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Positive regulation by small RNAs and the role of Hfq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes

28 July 2018

1 reference

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

28 July 2018

1 reference

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Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

The RNA binding protein Hfq interacts specifically with tRNAs.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Hfq stimulates the activity of the CCA-adding enzyme.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Identification of small Hfq-binding RNAs in Listeria monocytogenes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Strategies for RNA folding and assembly

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Global analysis of small RNA and mRNA targets of Hfq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Hfq affects the length and the frequency of short oligo(A) tails at the 3' end of Escherichia coli rpsO mRNAs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. Evidence for its generation in vivo by transcription termination and by RNase III and RNase E-dependent processing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Widespread suppression of intragenic transcription initiation by H-NS.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Antisense transcription is pervasive but rarely conserved in enteric bacteria

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Tn10/IS10 transposition is downregulated at the level of transposase expression by the RNA‐binding protein Hfq

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Next generation software for functional trend analysis

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

GadY, a small-RNA regulator of acid response genes in Escherichia coli

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Interaction of Escherichia coli RNA polymerase with the ribosomal protein S1 and the Sm-like ATPase Hfq.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

Identification of novel small RNAs using comparative genomics and microarrays

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4152368

28 October 2018

Identifiers

DOI

10.4161/RNA.29299

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31 July 2017

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31 July 2017

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