ArticleProceedings of the National Academy of Sciences of the United States of America2011
Quantifying the sequence-function relation in gene silencing by bacterial small RNAs.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 51 citations in OpenAlex.
- Crowdsourced riboregulators reveal design principles for programmable RNA switching.bioRxiv : the preprint server for biology · 2026Article
- A portable Cas6f-based system for multiplex translational repression in bacteria.Nature communications · 2026Article
- Advances in biotechnological methods for genetic and metabolic engineering in Methylomonas sp. DH-1.Journal of biological engineering · 2026Review
- What makes a small RNA work?Nucleic acids research · 2025Review
- Stepwise sRNA targeting of structured bacterial mRNAs leads to abortive annealing.Molecular cell · 2021Article
- Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH-1.Biotechnology for biofuels · 2020Article
- Digitalizing heterologous gene expression in Gram-negative bacteria with a portable ON/OFF module.Molecular systems biology · 2019Article
- Hfq-dependent mRNA unfolding promotes sRNA-based inhibition of translation.The EMBO journal · 2019Article
- A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions.Scientific reports · 2018Article
- Hfq chaperone brings speed dating to bacterial sRNA.Wiley interdisciplinary reviews. RNA · 2018Review
- Divergence of functional effects among bacterial sRNA paralogs.BMC evolutionary biology · 2017Article
- RNA search engines empower the bacterial intranet.Biochemical Society transactions · 2017Review
- Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli.Nucleic acids research · 2016Article
- Effects of cooperation between translating ribosome and RNA polymerase on termination efficiency of the Rho-independent terminator.Nucleic acids research · 2016Article
- Probing the Limits to MicroRNA-Mediated Control of Gene Expression.PLoS computational biology · 2016Article
- Paradoxical suppression of small RNA activity at high Hfq concentrations due to random-order binding.Nucleic acids research · 2015Article
- Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells.Biophysical journal · 2015Article
- Modelling toehold-mediated RNA strand displacement.Biophysical journal · 2015Article
- Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity.Nucleic acids research · 2014Article
- Phenotypic characterization of Salmonella RyhB-1 mutations that modulate target regulation.Current microbiology · 2014Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
Abstract
Sequence-function relations for small RNA (sRNA)-mediated gene silencing were quantified for the sRNA RyhB and some of its mRNA targets in Escherichia coli. Numerous mutants of RyhB and its targets were generated and their in vivo functions characterized at various levels of target and RyhB expression. Although a core complementary region is required for repression by RyhB, variations in the complementary sequences of the core region gave rise to a continuum of repression strengths, correlated exponentially with the computed free energy of RyhB-target duplex formation. Moreover, sequence variations in the linker region known to interact with the RNA chaperone Hfq also gave rise to a continuum of repression strengths, correlated exponentially with the computed energy cost of keeping the linker region open. These results support the applicability of the thermodynamic model in predicting sRNA-mRNA interaction and suggest that sequences at these locations may be used to fine-tune the degree of repression. Surprisingly, a truncated RyhB without the Hfq-binding region is found to repress multiple targets of the wild-type RyhB effectively, both in the presence and absence of Hfq, even though the former is required for the activity of wild-type RyhB itself. These findings challenge the commonly accepted model concerning the function of Hfq in gene silencing-both in providing stability to the sRNAs and in catalyzing the target mRNAs to take on active conformations-and raise the intriguing question of why many endogenous sRNAs subject their functions to Hfq-dependences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.