The conserved 3′ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration

Mimicry, deception and competition: The life of competing endogenous RNAs

(2019) Marc P. Grüll et al.   Wiley Interdisciplinary Reviews-RNA

A conserved RNA seed‐pairing domain directs small RNA‐mediated stress resistance in enterobacteria

(2019) Nikolai Peschek et al.   EMBO JOURNAL

RsaC sRNA modulates the oxidative stress response of Staphylococcus aureus during manganese starvation

(2019) David Lalaouna et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry

(2018) Jean-Benoît Lalanne et al.   CELL

New aspects of RNA-based regulation by Hfq and its partner sRNAs

(2018) Kumari Kavita et al.   CURRENT OPINION IN MICROBIOLOGY

Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3′ Ends

(2018) Erik Holmqvist et al.   MOLECULAR CELL

PcrX, an sRNA derived from the 3′- UTR of the Rhodobacter sphaeroides puf operon modulates expression of puf genes encoding proteins of the bacterial photosynthetic apparatus

(2018) Katrin Eisenhardt et al.   MOLECULAR MICROBIOLOGY

RNA-binding proteins in bacteria

(2018) Erik Holmqvist et al.   NATURE REVIEWS MICROBIOLOGY

Functional expansion of a TCA cycle operon mRNA by a 3′ end-derived small RNA

(2018) Masatoshi Miyakoshi et al.   NUCLEIC ACIDS RESEARCH

Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA

(2018) François De Mets et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanistic study of base-pairing small regulatory RNAs in bacteria

(2017) Jonathan Jagodnik et al.   METHODS

In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways

(2017) Yanjie Chao et al.   MOLECULAR CELL

ProQ/FinO-domain proteins: another ubiquitous family of RNA matchmakers?

(2017) Mikolaj Olejniczak et al.   MOLECULAR MICROBIOLOGY

Regulation of mRNA Decay in Bacteria

(2016) Bijoy K. Mohanty et al.   Annual Review of Microbiology

Nitrate, nitrite and nitric oxide reductases: from the last universal common ancestor to modern bacterial pathogens

(2016) Andrés Vázquez-Torres et al.   CURRENT OPINION IN MICROBIOLOGY

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E

(2016) Shafagh A Waters et al.   EMBO JOURNAL

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinkingin vivo

(2016) Erik Holmqvist et al.   EMBO JOURNAL

A feed-forward loop between SroC and MgrR small RNAs modulates the expression of eptB and the susceptibility to polymyxin B in Salmonella Typhimurium

(2016) Lillian G. Acuña et al.   MICROBIOLOGY-SGM

Global Mapping of Small RNA-Target Interactions in Bacteria

(2016) Sahar Melamed et al.   MOLECULAR CELL

A 3′ UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response

(2016) Yanjie Chao et al.   MOLECULAR CELL

Protection against deleterious nitrogen compounds: role of σS-dependent small RNAs encoded adjacent tosdiA

(2016) Yue Hao et al.   NUCLEIC ACIDS RESEARCH

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein

(2016) Alexandre Smirnov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase genenifKmRNA inPseudomonas stutzeriA1501

(2016) Yuhua Zhan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of a polyamine transporter by the conserved 3′ UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides inRhodobacter sphaeroides

(2016) Tao Peng et al.   RNA Biology

The ribonuclease polynucleotide phosphorylase can interact with small regulatory RNAs in both protective and degradative modes

(2016) Katarzyna J. Bandyra et al.   RNA

The CpxQ sRNA Negatively Regulates Skp To Prevent Mistargeting of β-Barrel Outer Membrane Proteins into the Cytoplasmic Membrane

(2016) Marcin Grabowicz et al.   mBio

The Pyromaniac Inside You:SalmonellaMetabolism in the Host Gut

(2015) Fabian Rivera-Chávez et al.   Annual Review of Microbiology

Structure of Bacterial Regulatory RNAs Determines Their Performance in Competition for the Chaperone Protein Hfq

(2015) Ewelina M. Małecka et al.   BIOCHEMISTRY

Regulatory small RNAs from the 3′ regions of bacterial mRNAs

(2015) Masatoshi Miyakoshi et al.   CURRENT OPINION IN MICROBIOLOGY

Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA

(2015) M. Miyakoshi et al.   EMBO JOURNAL

Codon Bias as a Means to Fine-Tune Gene Expression

(2015) Tessa E.F. Quax et al.   MOLECULAR CELL

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

(2015) Stephan Klähn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA reflections: converging on Hfq

(2015) Susan Gottesman et al.   RNA

Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK

(2015) Masahiro Fukuda et al.   Nature Communications

Messenger RNA Degradation in Bacterial Cells

(2014) Monica P. Hui et al.   Annual Review of Genetics

MicL, a new  E-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein

(2014) M. S. Guo et al.   GENES & DEVELOPMENT

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

(2014) Patrick R. Wright et al.   NUCLEIC ACIDS RESEARCH

Revisiting the coding potential of theE. coligenome through Hfq co-immunoprecipitation

(2014) Ivana Bilusic et al.   RNA Biology

Recognition of the small regulatory RNA RydC by the bacterial Hfq protein

(2014) Daniela Dimastrogiovanni et al.   eLife

Small RNA-Mediated Activation of Sugar Phosphatase mRNA Regulates Glucose Homeostasis

(2013) Kai Papenfort et al.   CELL

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

(2013) Carsten Kröger et al.   Cell Host & Microbe

Inverse regulation of Fe- and Ni-containing SOD genes by a Fur family regulator Nur through small RNA processed from 3′UTR of the sodF mRNA

(2013) Hae Mi Kim et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics boosts target prediction for bacterial small RNAs

(2013) P. R. Wright et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New developments in post-transcriptional regulation of operons by small RNAs

(2013) Divya Balasubramanian et al.   RNA Biology

Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

(2013) Kevin S. Myers et al.   PLoS Genetics

Multiple factors dictate target selection by Hfq-binding small RNAs

(2012) Chase L Beisel et al.   EMBO JOURNAL

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

(2012) Yanjie Chao et al.   EMBO JOURNAL

Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA

(2012) Colin P. Corcoran et al.   MOLECULAR MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RNase E: at the interface of bacterial RNA processing and decay

(2012) George A. Mackie   NATURE REVIEWS MICROBIOLOGY

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

(2012) C. Kroger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3' poly(U) tail

(2012) H. Ishikawa et al.   RNA

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD

(2011) Kathrin S. Fröhlich et al.   NUCLEIC ACIDS RESEARCH

Structural basis for RNA 3′-end recognition by Hfq

(2011) Evelyn Sauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAs actively cycle on the Sm-like protein Hfq

(2010) A. Fender et al.   GENES & DEVELOPMENT

Reprogramming of anaerobic metabolism by the FnrS small RNA

(2010) Sylvain Durand et al.   MOLECULAR MICROBIOLOGY

Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA

(2009) Guillaume Desnoyers et al.   EMBO JOURNAL

Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

(2009) N. Figueroa-Bossi et al.   GENES & DEVELOPMENT

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Small RNA Binding to 5′ mRNA Coding Region Inhibits Translational Initiation

(2008) Marie Bouvier et al.   MOLECULAR CELL

The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli

(2008) Birte Reichenbach et al.   NUCLEIC ACIDS RESEARCH

Two Seemingly Homologous Noncoding RNAs Act Hierarchically to Activate glmS mRNA Translation

(2008) Johannes H Urban et al.   PLOS BIOLOGY