Published in Proc Natl Acad Sci U S A on November 08, 2010
Hfq and its constellation of RNA. Nat Rev Microbiol (2011) 4.94
Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell (2011) 4.68
A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics. Cell (2015) 2.31
An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs. EMBO J (2012) 2.10
Structural basis for RNA 3'-end recognition by Hfq. Proc Natl Acad Sci U S A (2011) 1.73
Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol (2012) 1.66
Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition. Proc Natl Acad Sci U S A (2012) 1.51
The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell (2012) 1.49
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon. Proc Natl Acad Sci U S A (2011) 1.46
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure (2011) 1.36
Quorum-sensing non-coding small RNAs use unique pairing regions to differentially control mRNA targets. Mol Microbiol (2012) 1.32
De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc Natl Acad Sci U S A (2012) 1.31
Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A (2013) 1.29
Multiple factors dictate target selection by Hfq-binding small RNAs. EMBO J (2012) 1.27
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res (2011) 1.23
MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein. Genes Dev (2014) 1.21
Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions. J Bacteriol (2011) 1.19
Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. Genes Dev (2012) 1.16
Structure and RNA-binding properties of the bacterial LSm protein Hfq. RNA Biol (2013) 1.16
RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med (2013) 1.11
Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA. EMBO J (2015) 1.11
Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition. EMBO J (2015) 1.08
Small RNA functions in carbon metabolism and virulence of enteric pathogens. Front Cell Infect Microbiol (2014) 1.08
sRNAs and the virulence of Salmonella enterica serovar Typhimurium. RNA Biol (2012) 1.04
Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? RNA Biol (2012) 1.04
The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci U S A (2012) 1.04
Functional determinants of the quorum-sensing non-coding RNAs and their roles in target regulation. EMBO J (2013) 1.03
The social fabric of the RNA degradosome. Biochim Biophys Acta (2013) 1.02
A small RNA activates CFA synthase by isoform-specific mRNA stabilization. EMBO J (2013) 1.02
Post-transcriptional control of the Escherichia coli PhoQ-PhoP two-component system by multiple sRNAs involves a novel pairing region of GcvB. PLoS Genet (2013) 1.01
Recognition of the small regulatory RNA RydC by the bacterial Hfq protein. Elife (2014) 0.98
How do base-pairing small RNAs evolve? FEMS Microbiol Rev (2015) 0.93
A survey of sRNA families in α-proteobacteria. RNA Biol (2012) 0.87
Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics (2014) 0.87
Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Res (2015) 0.86
Essential requirements for robust signaling in Hfq dependent small RNA networks. PLoS Comput Biol (2011) 0.86
The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum. BMC Genomics (2013) 0.85
Functional characterization of the type III secretion ATPase SsaN encoded by Salmonella pathogenicity island 2. PLoS One (2014) 0.84
The ZorO-OrzO type I toxin-antitoxin locus: repression by the OrzO antitoxin. Nucleic Acids Res (2013) 0.84
NAPP: the Nucleic Acid Phylogenetic Profile Database. Nucleic Acids Res (2011) 0.83
Small RNA modules confer different stabilities and interact differently with multiple targets. PLoS One (2013) 0.83
Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti. PLoS One (2013) 0.83
RNA binding by Hfq and ring-forming (L)Sm proteins: a trade-off between optimal sequence readout and RNA backbone conformation. RNA Biol (2014) 0.82
Cell-based assay to identify inhibitors of the Hfq-sRNA regulatory pathway. Antimicrob Agents Chemother (2014) 0.81
Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region. RNA Biol (2014) 0.81
Identifying and characterizing Hfq-RNA interactions. Methods (2013) 0.81
Multi-target regulation by small RNAs synchronizes gene expression thresholds and may enhance ultrasensitive behavior. PLoS One (2012) 0.80
The VrrA sRNA controls a stationary phase survival factor Vrp of Vibrio cholerae. RNA Biol (2015) 0.80
Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis by Deep Sequencing. J Bacteriol (2015) 0.79
Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis. Front Microbiol (2015) 0.79
The multicopy sRNA LhrC controls expression of the oligopeptide-binding protein OppA in Listeria monocytogenes. RNA Biol (2015) 0.79
The sRNA RyhB regulates the synthesis of the Escherichia coli methionine sulfoxide reductase MsrB but not MsrA. PLoS One (2013) 0.78
The target spectrum of SdsR small RNA in Salmonella. Nucleic Acids Res (2016) 0.76
Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli. BMC Genomics (2015) 0.76
Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assembly in vivo. Front Life Sci (2013) 0.75
Neisseria meningitidis Uses Sibling Small Regulatory RNAs To Switch from Cataplerotic to Anaplerotic Metabolism. MBio (2017) 0.75
Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure. RNA (2016) 0.75
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. Nucleic Acids Res (2017) 0.75
MicroRNAs: target recognition and regulatory functions. Cell (2009) 92.17
Most mammalian mRNAs are conserved targets of microRNAs. Genome Res (2008) 37.16
Fast and effective prediction of microRNA/target duplexes. RNA (2004) 18.10
Regulatory RNAs in bacteria. Cell (2009) 9.57
A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proc Natl Acad Sci U S A (1984) 8.67
Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev (2003) 7.33
The path of messenger RNA through the ribosome. Cell (2001) 5.65
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet (2008) 5.23
Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol (2003) 4.98
The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol (2004) 4.88
mRNA helicase activity of the ribosome. Cell (2005) 4.72
A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. Cell (1997) 4.64
Conserved and variable functions of the sigmaE stress response in related genomes. PLoS Biol (2006) 4.46
Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol (2005) 4.01
RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev (2005) 3.66
Hfq structure, function and ligand binding. Curr Opin Microbiol (2007) 3.49
The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium. Mol Microbiol (2006) 3.35
A 5'-terminal stem-loop structure can stabilize mRNA in Escherichia coli. Genes Dev (1992) 3.15
The use of RNAs complementary to specific mRNAs to regulate the expression of individual bacterial genes. Cell (1984) 3.15
SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol (2006) 3.07
Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res (2007) 3.06
Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol (2007) 2.93
Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev (2005) 2.93
Small RNA binding to 5' mRNA coding region inhibits translational initiation. Mol Cell (2008) 2.88
Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev (2002) 2.75
Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Mol Microbiol (2006) 2.69
Antisense RNAs in bacteria and their genetic elements. Adv Genet (2002) 2.68
Initiation of RNA decay in Escherichia coli by 5' pyrophosphate removal. Mol Cell (2007) 2.55
MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol (2004) 2.53
A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev (2007) 2.44
Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol (2009) 2.25
Target identification of small noncoding RNAs in bacteria. Curr Opin Microbiol (2007) 2.20
Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins. J Mol Biol (2006) 2.18
Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc Natl Acad Sci U S A (2006) 2.08
A rough guide to the non-coding RNA world of Salmonella. Mol Microbiol (2008) 1.89
Footprinting mRNA-ribosome complexes with chemical probes. EMBO J (1994) 1.84
SigmaE regulates and is regulated by a small RNA in Escherichia coli. J Bacteriol (2007) 1.68
The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator. Nucleic Acids Res (2008) 1.63
Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis. Mol Microbiol (2008) 1.62
Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding. EMBO J (2007) 1.55
Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA. EMBO J (2009) 1.55
Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis. EMBO J (2010) 1.53
Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level. Res Microbiol (2009) 1.46
Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol Microbiol (2010) 1.46
A small RNA downregulates LamB maltoporin in Salmonella. Mol Microbiol (2007) 1.44
Sigma E controls biogenesis of the antisense RNA MicA. Nucleic Acids Res (2007) 1.38
The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli. J Bacteriol (2004) 1.25
Secondary structures of Escherichia coli antisense micF RNA, the 5'-end of the target ompF mRNA, and the RNA/RNA duplex. Biochemistry (1995) 1.25
MicA sRNA links the PhoP regulon to cell envelope stress. Mol Microbiol (2010) 1.22
Small RNA-mediated regulation at the level of transcript stability. RNA Biol (2010) 1.22
Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli. J Biol Chem (2010) 1.19
Promoter strength properties of the complete sigma E regulon of Escherichia coli and Salmonella enterica. J Bacteriol (2009) 1.19
How the ribosome moves along the mRNA during protein synthesis. J Biol Chem (1994) 1.11
Quantifying mRNA synthesis and decay rates using small RNAs. Biophys J (2010) 0.82
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature (2011) 17.38
The primary transcriptome of the major human pathogen Helicobacter pylori. Nature (2010) 7.70
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet (2008) 5.23
Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell (2011) 4.68
Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24
The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium. Mol Microbiol (2006) 3.35
SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol (2006) 3.07
Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res (2007) 3.06
Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev (2005) 2.93
Small RNA binding to 5' mRNA coding region inhibits translational initiation. Mol Cell (2008) 2.88
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A (2011) 2.84
Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol (2008) 2.61
The single-stranded genome of phage CTX is the form used for integration into the genome of Vibrio cholerae. Mol Cell (2005) 2.55
Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell (2013) 2.52
A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev (2007) 2.44
Microanatomy at cellular resolution and spatial order of physiological differentiation in a bacterial biofilm. MBio (2013) 2.43
Regulatory RNA in bacterial pathogens. Cell Host Microbe (2010) 2.41
The role of Hfq in bacterial pathogens. Curr Opin Microbiol (2010) 2.40
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A (2012) 2.39
Dual RNA-seq of pathogen and host. Nat Rev Microbiol (2012) 2.32
Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol (2009) 2.25
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res (2009) 2.20
An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs. EMBO J (2012) 2.10
Activation of gene expression by small RNA. Curr Opin Microbiol (2009) 2.04
Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family. EMBO J (2011) 2.03
Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res (2010) 1.99
An antisense RNA inhibits translation by competing with standby ribosomes. Mol Cell (2007) 1.97
Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol (2009) 1.92
A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles. Mol Microbiol (2008) 1.83
Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol (2005) 1.82
Experimental approaches to identify non-coding RNAs. Nucleic Acids Res (2006) 1.80
Structural basis for broad DNA-specificity in integron recombination. Nature (2006) 1.79
Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol (2009) 1.77
A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome. Mol Microbiol (2007) 1.72
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet (2013) 1.67
Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci U S A (2009) 1.66
Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol (2011) 1.64
Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res (2007) 1.62
Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis. Mol Microbiol (2008) 1.62
RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq. Proc Natl Acad Sci U S A (2012) 1.54
Comparative study of class 1 integron and Vibrio cholerae superintegron integrase activities. J Bacteriol (2005) 1.52
The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell (2012) 1.49
Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res (2010) 1.49
The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase. Plant Cell (2012) 1.47
Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level. Res Microbiol (2009) 1.46
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon. Proc Natl Acad Sci U S A (2011) 1.46
Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biol (2009) 1.42
Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell (2013) 1.39
Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol Microbiol (2012) 1.29
Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A (2013) 1.29
Noncoding RNA control of the making and breaking of sugars. Genes Dev (2008) 1.28
The mammalian microRNA response to bacterial infections. RNA Biol (2012) 1.27
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res (2011) 1.25
A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis. J Mol Biol (2007) 1.24
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res (2011) 1.23
Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet (2012) 1.17
The transcriptional landscape of Chlamydia pneumoniae. Genome Biol (2011) 1.16
Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing. Nucleic Acids Res (2012) 1.16
In vivo expression and purification of aptamer-tagged small RNA regulators. Nucleic Acids Res (2009) 1.15
Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol (2011) 1.15
RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med (2013) 1.11
Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides. Mol Microbiol (2009) 1.10
Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol (2012) 1.08
Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA. Genes Dev (2013) 1.07
Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides. Mol Microbiol (2011) 1.05
The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci U S A (2012) 1.04
The cyanobacterial homologue of the RNA chaperone Hfq is essential for motility of Synechocystis sp. PCC 6803. Microbiology (2008) 1.02
A small RNA activates CFA synthase by isoform-specific mRNA stabilization. EMBO J (2013) 1.02
The social fabric of the RNA degradosome. Biochim Biophys Acta (2013) 1.02
Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression. Silence (2011) 0.98
The csgD mRNA as a hub for signal integration via multiple small RNAs. Mol Microbiol (2012) 0.95
Functional characterization of the RNA chaperone Hfq in the opportunistic human pathogen Stenotrophomonas maltophilia. J Bacteriol (2012) 0.95
In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis. RNA Biol (2011) 0.94
Acid stress activation of the sigma(E) stress response in Salmonella enterica serovar Typhimurium. Mol Microbiol (2009) 0.93
An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains. Nucleic Acids Res (2012) 0.93
A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori. Proc Natl Acad Sci U S A (2014) 0.92
Concerted action of plasmid maintenance functions: partition complexes create a requirement for dimer resolution. Mol Microbiol (2006) 0.91
Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis. BMC Genomics (2014) 0.90
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression. BMC Genomics (2012) 0.90