ArticleRNA (New York, N.Y.)2014
Detecting translational regulation by change point analysis of ribosome profiling data sets.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 39 citations in OpenAlex.
- New insights into the efficient secretion of foreign protein in Bacillus subtilis via Ribo-seq and RNA-seq integrative analyses.BMC microbiology · 2024Article
- ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events.BMC bioinformatics · 2023Article
- Article
- Luciferase-based reporter system for in vitro evaluation of elongation rate and processivity of ribosomes.Nucleic acids research · 2021Article
- Translational regulation contributes to the secretory response of chondrocytic cells following exposure to interleukin-1β.The Journal of biological chemistry · 2019Article
- Cell-Type-Specific Profiling of Alternative Translation Identifies Regulated Protein Isoform Variation in the Mouse Brain.Cell reports · 2019Article
- Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events.Nucleic acids research · 2018Article
- Following Ribosome Footprints to Understand Translation at a Genome Wide Level.Computational and structural biotechnology journal · 2018Review
- Ribo-seq enlightens codon usage bias.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects ofFrontiers in microbiology · 2017Review
- Leveraging genome-wide datasets to quantify the functional role of the anti-Shine-Dalgarno sequence in regulating translation efficiency.Open biology · 2017Article
- A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics.PloS one · 2017Article
- Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution.Nucleic acids research · 2016Article
- Modeling and gene knockdown to assess the contribution of nonsense-mediated decay, premature termination, and selenocysteine insertion to the selenoprotein hierarchy.RNA (New York, N.Y.) · 2016Article
- Article
- Detecting actively translated open reading frames in ribosome profiling data.Nature methods · 2016Article
- RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Ribo-Seq maps the location of translating ribosomes on mature mRNA transcripts. While during normal translation, ribosome density is constant along the length of the mRNA coding region, this can be altered in response to translational regulatory events. In the present study, we developed a method to detect translational regulation of individual mRNAs from their ribosome profiles, utilizing changes in ribosome density. We used mathematical modeling to show that changes in ribosome density should occur along the mRNA at the point of regulation. We analyzed a Ribo-Seq data set obtained for mouse embryonic stem cells and showed that normalization by corresponding RNA-Seq can be used to improve the Ribo-Seq quality by removing bias introduced by deep-sequencing and alignment artifacts. After normalization, we applied a change point algorithm to detect changes in ribosome density present in individual mRNA ribosome profiles. Additional sequence and gene isoform information obtained from the UCSC Genome Browser allowed us to further categorize the detected changes into different mechanisms of regulation. In particular, we detected several mRNAs with known post-transcriptional regulation, e.g., premature termination for selenoprotein mRNAs and translational control of Atf4, but also several more mRNAs with hitherto unknown translational regulation. Additionally, our approach proved useful for identification of new transcript isoforms.
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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.