ArticleRNA (New York, N.Y.)2015
The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed, 162 citations in OpenAlex.
- Integrated Analysis of Rat Pulmonary Hypertension Datasets Identifies Candidate circRNA Networks in Hypoxia-Exposed Pulmonary Artery Tissue.International journal of molecular sciences · 2026Article
- Ribo-seq rRNA reads reveal co-predicted signatures of ribosome heterogeneity and collisions.Briefings in bioinformatics · 2026Article
- Data-driven design of LNA-blockers for efficient contaminant removal in Ribo-Seq libraries.Scientific reports · 2026Article
- The Salmonella pathogenicity island 1 injectisome reprograms host cell translation to evade the inflammatory response.Nature communications · 2025Article
- Optimised Ribosome Profiling Reveals New Insights Into Translational Regulation in Synchronised Chlamydomonas reinhardtii Cultures.Plant, cell & environment · 2025Article
- Advances in ribosome profiling technologies.Biochemical Society transactions · 2025Review
- Zika viruses encode 5' upstream open reading frames affecting infection of human brain cells.Nature communications · 2024Article
- Optimization of ribosome profiling in plants including structural analysis of rRNA fragments.Plant methods · 2024Article
- Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts.Nature communications · 2024Article
- A novel ilarvirus protein CP-RT is expressed via stop codon readthrough and suppresses RDR6-dependent RNA silencing.PLoS pathogens · 2024Article
- Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis.The Plant cell · 2024Article
- Ribosome Profiling of Plants.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Genome-Wide Identification, Evolutionary Analysis, and Functional Studies ofInternational journal of molecular sciences · 2023Article
- The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria.Nature communications · 2023Article
- What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?Molecular & cellular proteomics : MCP · 2023Article
- RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing - 2023 Update.Journal of molecular biology · 2023Article
- What can Ribo-seq and proteomics tell us about the non-canonical proteome?bioRxiv : the preprint server for biology · 2023Article
- Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum.BMC biology · 2023Article
- Discovering microproteins: making the most of ribosome profiling data.RNA biology · 2023Review
- Genome-wide identification, evolution, and expression analysis ofFrontiers in plant science · 2023Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination. We show that DSN-based depletion compares favorably with other commonly used rRNA depletion strategies and introduces little bias. The profiling protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream, and overlapping open reading frames (ORFs) and an alternative ribosome conformation evident during termination of protein synthesis. In addition, we provide a software package that presents a set of methods for parsing ribosomal profiling data from multiple samples, aligning reads to coding sequences, inferring alternative ORFs, and plotting average and transcript-specific aspects of the data. Methods are also provided for extracting the data in a form suitable for differential analysis of translation and translational efficiency.
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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.