Bacterial regulatory RNAs: complexity, function, and putative drug targeting

Transcriptional interference by small transcripts in proximal promoter regions

(2018) Amit Pande et al.   NUCLEIC ACIDS RESEARCH

Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

(2017) Gang Sheng et al.   NUCLEIC ACIDS RESEARCH

Resolving host–pathogen interactions by dual RNA-seq

(2017) Alexander J. Westermann et al.   PLoS Pathogens

sRNA-mediated activation of gene expression by inhibition of 5'-3’ exonucleolytic mRNA degradation

(2017) Sylvain Durand et al.   eLife

sRNA-Mediated Control of Transcription Termination in E. coli

(2016) Nadezda Sedlyarova et al.   CELL

CncRNAs: RNAs with both coding and non-coding roles in development

(2016) Karuna Sampath et al.   DEVELOPMENT

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

Global Mapping of Small RNA-Target Interactions in Bacteria

(2016) Sahar Melamed et al.   MOLECULAR CELL

Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

(2016) Alexander J. Westermann et al.   NATURE

A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes

(2016) Roi Avraham et al.   Nature Protocols

RNA modifications: what have we learned and where are we headed?

(2016) Michaela Frye et al.   NATURE REVIEWS GENETICS

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

What is an RNA?A top layer for RNA classification

(2016) Jürgen Brosius et al.   RNA Biology

RNA-based mechanisms of virulence control in Enterobacteriaceae

(2016) Ann Kathrin Heroven et al.   RNA Biology

GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation

(2016) Kook Han et al.   Nature Microbiology

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

(2015) Lars Barquist et al.   Annual Review of Genetics

Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing

(2015) Rienk A Rienksma et al.   BMC GENOMICS

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

Regulatory small RNAs from the 3′ regions of bacterial mRNAs

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

A 3′ External Transcribed Spacer in a tRNA Transcript Acts as a Sponge for Small RNAs to Prevent Transcriptional Noise

(2015) David Lalaouna et al.   MOLECULAR CELL

cncRNAs: Bi-functional RNAs with protein coding and non-coding functions

(2015) Pooja Kumari et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Unexpected versatility in bacterial riboswitches

(2015) J.R. Mellin et al.   TRENDS IN GENETICS

Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk

(2015) B. Baddal et al.   mBio

The bacterial proteogenomic pipeline

(2014) Julian Uszkoreit et al.   BMC GENOMICS

Bacterial and cellular RNAs at work during Listeria infection

(2014) Nina Sesto et al.   Future Microbiology

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

Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli

(2014) Jai J. Tree et al.   MOLECULAR CELL

Quorum regulatory small RNAs repress type VI secretion inVibrio cholerae

(2014) Yi Shao et al.   MOLECULAR MICROBIOLOGY

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

Dual RNA regulatory control of a Staphylococcus aureus virulence factor

(2014) Svetlana Chabelskaya et al.   NUCLEIC ACIDS RESEARCH

The double-stranded transcriptome of Escherichia coli

(2014) M. Lybecker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Duplex formation between the sRNA DsrA andrpoSmRNA is not sufficient for efficient RpoS synthesis at low temperature

(2014) Hermann Hämmerle et al.   RNA Biology

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

(2014) Ivana Bilusic et al.   RNA Biology

Dual Toxic-Peptide-Coding Staphylococcus aureus RNA under Antisense Regulation Targets Host Cells and Bacterial Rivals Unequally

(2014) Marie-Laure Pinel-Marie et al.   Cell Reports

Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa Carbon Catabolite Repression

(2014) Elisabeth Sonnleitner et al.   PLoS Genetics

Regulatory RNAs Involved in Bacterial Antibiotic Resistance

(2014) David Lalaouna et al.   PLoS Pathogens

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis

(2014) Luis Solans et al.   PLoS Pathogens

Small RNA functions in carbon metabolism and virulence of enteric pathogens

(2014) Kai Papenfort et al.   Frontiers in Cellular and Infection Microbiology

Antibiotic drugs targeting bacterial RNAs

(2014) Weiling Hong et al.   Acta Pharmaceutica Sinica B

RIP-seq of BmAgo2-associated small RNAs reveal various types of small non-coding RNAs in the silkworm, Bombyx mori

(2013) Zuoming Nie et al.   BMC GENOMICS

Functional transcriptomics in the post-ENCODE era

(2013) J. M. Mudge et al.   GENOME RESEARCH

Analysis of the Proteome of Intracellular Shigella flexneri Reveals Pathways Important for Intracellular Growth

(2013) Rembert Pieper et al.   INFECTION AND IMMUNITY

Bacterial sRNAs: Regulation in stress

(2013) Chee-Hock Hoe et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Prospects for new antibiotics: a molecule-centered perspective

(2013) Christopher T Walsh et al.   JOURNAL OF ANTIBIOTICS

Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq

(2013) Sabarinath Jayaseelan et al.   METHODS

To be or not to be: regulation of restriction–modification systems and other toxin–antitoxin systems

(2013) Iwona Mruk et al.   NUCLEIC ACIDS RESEARCH

Effect of ribosome shielding on mRNA stability

(2013) Carlus Deneke et al.   PHYSICAL BIOLOGY

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

(2013) Michael S. Humphrys et al.   PLoS One

Bacterial Quorum Sensing: Its Role in Virulence and Possibilities for Its Control

(2013) S. T. Rutherford et al.   Cold Spring Harbor Perspectives in Medicine

RNA-Mediated Regulation in Pathogenic Bacteria

(2013) I. Caldelari et al.   Cold Spring Harbor Perspectives in Medicine

Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals

(2013) Roy R. Chaudhuri et al.   PLoS Genetics

Ribonuclease III mechanisms of double-stranded RNA cleavage

(2013) Allen W. Nicholson   Wiley Interdisciplinary Reviews-RNA

Transcription Analysis and Small Non-Protein Coding RNAs Associated with Bacterial Ribosomal Protein Operons

(2012) G.A. Khayrullina et al.   CURRENT MEDICINAL CHEMISTRY

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

(2012) Yanjie Chao et al.   EMBO JOURNAL

A role for Rho-dependent polarity in gene regulation by a noncoding small RNA

(2012) L. Bossi et al.   GENES & DEVELOPMENT

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

(2012) H. Tani et al.   GENOME RESEARCH

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

(2012) B. Ryall et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

The twin-arginine translocation (Tat) protein export pathway

(2012) Tracy Palmer et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial RNA thermometers: molecular zippers and switches

(2012) Jens Kortmann et al.   NATURE REVIEWS MICROBIOLOGY

Dual-acting riboswitch control of translation initiation and mRNA decay

(2012) M.-P. Caron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergently overlappingcis-encoded antisense RNA regulating toxin-antitoxin systems fromE. coli

(2012) Mitsuoki Kawano   RNA Biology

Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch

(2012) V. K. Boyapati et al.   RNA

Antisense Transcription Is Pervasive but Rarely Conserved in Enteric Bacteria

(2012) R. Raghavan et al.   mBio

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells

(2012) Lanay Tierney et al.   Frontiers in Microbiology

Novel classes of antibiotics or more of the same?

(2011) Anthony RM Coates et al.   BRITISH JOURNAL OF PHARMACOLOGY

Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence

(2011) D. A. Ravcheev et al.   JOURNAL OF BACTERIOLOGY

Novel Mycobacteria Antigen 85 Complex Binding Motif on Fibronectin

(2011) Chih-Jung Kuo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Functional Half-Life of an mRNA Depends on the Ribosome Spacing in an Early Coding Region

(2011) Margit Pedersen et al.   JOURNAL OF MOLECULAR BIOLOGY

cis-Antisense RNA, Another Level of Gene Regulation in Bacteria

(2011) J. Georg et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA

(2011) Cynthia M. Sharma et al.   MOLECULAR MICROBIOLOGY

RNA mimicry, a decoy for regulatory proteins

(2011) S. Marzi et al.   MOLECULAR MICROBIOLOGY

Termination and antitermination: RNA polymerase runs a stop sign

(2011) Thomas J. Santangelo et al.   NATURE REVIEWS MICROBIOLOGY

Hfq and its constellation of RNA

(2011) Jörg Vogel et al.   NATURE REVIEWS MICROBIOLOGY

A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide

(2011) Nour Sayed et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The small RNA SgrS controls sugar–phosphate accumulation by regulating multiple PTS genes

(2011) Jennifer B. Rice et al.   NUCLEIC ACIDS RESEARCH

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Major role for mRNA binding and restructuring in sRNA recruitment by Hfq

(2011) T. J. Soper et al.   RNA

The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome

(2011) C. A. Raabe et al.   RNA

Synthetic RNA Silencing in Bacteria ? Antimicrobial Discovery and Resistance Breaking

(2011) Liam Good et al.   Frontiers in Microbiology

Regulatory RNA in Bacterial Pathogens

(2010) Kai Papenfort et al.   Cell Host & Microbe

The role of Hfq in bacterial pathogens

(2010) Yanjie Chao et al.   CURRENT OPINION IN MICROBIOLOGY

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

RNAs actively cycle on the Sm-like protein Hfq

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

Mechanism of Positive Regulation by DsrA and RprA Small Noncoding RNAs: Pairing Increases Translation and Protects rpoS mRNA from Degradation

(2010) C. A. McCullen et al.   JOURNAL OF BACTERIOLOGY

VrrA Mediates Hfq-Dependent Regulation of OmpT Synthesis in Vibrio cholerae

(2010) Tianyan Song et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

MicA sRNA links the PhoP regulon to cell envelope stress

(2010) Audrey Coornaert et al.   MOLECULAR MICROBIOLOGY

A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon

(2010) Matthias Gimpel et al.   MOLECULAR MICROBIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

An allosteric mechanism of Rho-dependent transcription termination

(2010) Vitaly Epshtein et al.   NATURE

RNAs: regulators of bacterial virulence

(2010) Jonas Gripenland et al.   NATURE REVIEWS MICROBIOLOGY

A novel antisense RNA regulates at transcriptional level the virulence gene icsA of Shigella flexneri

(2010) Mara Giangrossi et al.   NUCLEIC ACIDS RESEARCH

Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi

(2010) Suresh V. Chinni et al.   NUCLEIC ACIDS RESEARCH

Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway

(2010) Sandra C. Viegas et al.   NUCLEIC ACIDS RESEARCH

Riboswitches: Structures and Mechanisms

(2010) A. D. Garst et al.   Cold Spring Harbor Perspectives in Biology

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

(2010) S. Gottesman et al.   Cold Spring Harbor Perspectives in Biology

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Bacterial Quorum-Sensing Network Architectures

(2009) Wai-Leung Ng et al.   Annual Review of Genetics

Regulation of Translation Initiation by RNA Binding Proteins

(2009) Paul Babitzke et al.   Annual Review of Microbiology

The Many Pathways of RNA Degradation

(2009) Jonathan Houseley et al.   CELL

A trans-Acting Riboswitch Controls Expression of the Virulence Regulator PrfA in Listeria monocytogenes

(2009) Edmund Loh et al.   CELL

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Quorum sensing and environmental adaptation in Pseudomonas aeruginosa: a tale of regulatory networks and multifunctional signal molecules

(2009) Paul Williams et al.   CURRENT OPINION IN MICROBIOLOGY

ncRNA transcription makes its mark

(2009) Grant A Hartzog et al.   EMBO JOURNAL

H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation

(2009) Marina Pinskaya et al.   EMBO JOURNAL

Subcellular localization of a bacterial regulatory RNA

(2009) J. H. Russell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa

(2009) E. Sonnleitner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of chemical modification on the potency, serum stability, and immunostimulatory properties of short shRNAs

(2009) Q. Ge et al.   RNA

Quorum Sensing in Staphylococci

(2008) Richard P. Novick et al.   Annual Review of Genetics

Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria

(2008) P M Bennett   BRITISH JOURNAL OF PHARMACOLOGY

Riboswitches: Ancient and Promising Genetic Regulators

(2008) Simon Blouin et al.   CHEMBIOCHEM

Overcoming the Innate Immune Response to Small Interfering RNA

(2008) Adam Judge et al.   HUMAN GENE THERAPY

Lysine Represses Transcription of the Escherichia coli dapB Gene by Preventing Its Activation by the ArgP Activator

(2008) J. Bouvier et al.   JOURNAL OF BACTERIOLOGY

The Crp-Activated Small Noncoding Regulatory RNA CyaR (RyeE) Links Nutritional Status to Group Behavior

(2008) N. De Lay et al.   JOURNAL OF BACTERIOLOGY

Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis

(2008) Kai Papenfort et al.   MOLECULAR MICROBIOLOGY

A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles

(2008) Tianyan Song et al.   MOLECULAR MICROBIOLOGY

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes

(2008) Hsi-Yuan Huang et al.   NUCLEIC ACIDS RESEARCH

Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence

(2008) Gilly Padalon-Brauch et al.   NUCLEIC ACIDS RESEARCH

The 5′ end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator

(2008) Maude Guillier et al.   NUCLEIC ACIDS RESEARCH