ArticleBioinformatics (Oxford, England)2013
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- TRAINSPOTTER: profiling nascent protein N-termini indicative of bacterial translation initiation via deformylation-assisted N-terminomics.Nucleic acids research · 2026Article
- Comprehensive analysis of yeast +1 ribosomal frameshifting unveils a novel stimulator supporting two distinct frameshifting mechanisms.Nucleic acids research · 2025Article
- Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection.Microbiology spectrum · 2024Article
- Ribosome profiling: a powerful tool in oncological research.Biomarker research · 2024Review
- Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria.Nature communications · 2023Article
- Estimation of peptide elongation times from ribosome profiling spectra.Nucleic acids research · 2021Article
- Transcriptome and translatome of COScientific data · 2021Article
- Extending the Spacing between the Shine-Dalgarno Sequence and P-Site Codon Reduces the Rate of mRNA Translocation.Journal of molecular biology · 2020Article
- Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5' mRNA Stem-Loop and Enhanced Drop-off.Journal of molecular biology · 2020Article
- Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?RNA biology · 2020Article
- Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming.Scientific reports · 2019Article
- DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns.Nucleic acids research · 2019Article
- Optimization of ribosome profiling using low-input brain tissue from fragile X syndrome model mice.Nucleic acids research · 2019Article
- A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution.eLife · 2019Article
- PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data.RNA (New York, N.Y.) · 2018Article
- Translation Elongation Factor 4 (LepA) Contributes to Tetracycline Susceptibility by Stalling Elongating Ribosomes.Antimicrobial agents and chemotherapy · 2018Article
- The translational landscape of Arabidopsis mitochondria.Nucleic acids research · 2018Article
- GWIPS-viz: 2018 update.Nucleic acids research · 2018Article
- Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria.Methods in enzymology · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationRibosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine-Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints.
resultsHere, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3'-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data.
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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.