ArticleNucleic acids research2015
Identification of bacterial sRNA regulatory targets using ribosome profiling.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 79 citations in OpenAlex.
- Coordination of the Fe-S cluster biogenesis network by the sRNA RyhB inRNA biology · 2025Article
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- Post-transcriptional regulation of aromatic amino acid metabolism by GcvB small RNA inMicrobiology spectrum · 2025Article
- Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity.Nucleic acids research · 2024Article
- Characterisation of sRNAs enriched in outer membrane vesicles of pathogenicJournal of extracellular biology · 2024Article
- CRISPR-dCas13a system for programmable small RNAs and polycistronic mRNA repression in bacteria.Nucleic acids research · 2024Article
- Characterization of theFrontiers in cellular and infection microbiology · 2024Article
- Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus.Methods in molecular biology (Clifton, N.J.) · 2024Article
- New RoxS sRNA Targets Identified in Bacillus subtilis by Pulsed SILAC.Microbiology spectrum · 2023Article
- High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5International journal of molecular sciences · 2022Article
- Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria.Science (New York, N.Y.) · 2022Article
- Inferring the contribution of small RNAs to changes in gene expression in response to stress.NAR genomics and bioinformatics · 2022Article
- Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling.Journal of bacteriology · 2022Article
- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism.RNA biology · 2022Article
- Recent Research Advances in Small Regulatory RNAs in Streptococcus.Current microbiology · 2021Review
- Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.The Journal of biological chemistry · 2020Article
- Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks.mSystems · 2020Article
- CopomuS-Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments.International journal of molecular sciences · 2020Article
- Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation.eLife · 2020Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Bacteria express large numbers of non-coding, regulatory RNAs known as 'small RNAs' (sRNAs). sRNAs typically regulate expression of multiple target messenger RNAs (mRNAs) through base-pairing interactions. sRNA:mRNA base-pairing often results in altered mRNA stability and/or altered translation initiation. Computational identification of sRNA targets is challenging due to the requirement for only short regions of base-pairing that can accommodate mismatches. Experimental approaches have been applied to identify sRNA targets on a genomic scale, but these focus only on those targets regulated at the level of mRNA stability. Here, we utilize ribosome profiling (Ribo-seq) to experimentally identify regulatory targets of the Escherichia coli sRNA RyhB. We not only validate a majority of known RyhB targets using the Ribo-seq approach, but also discover many novel ones. We further confirm regulation of a selection of known and novel targets using targeted reporter assays. By mutating nucleotides in the mRNA of a newly discovered target, we demonstrate direct regulation of this target by RyhB. Moreover, we show that Ribo-seq distinguishes between mRNAs regulated at the level of RNA stability and those regulated at the level of translation. Thus, Ribo-seq represents a powerful approach for genome-scale identification of sRNA targets.
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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.