ArticleGenome biology2019
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 42 citations in OpenAlex.
- Predicting the translation efficiency of messenger RNA in mammalian cells.Nature biotechnology · 2026Article
- Graded versus ON/OFF control in quantitative gene expression and epigenetic memory.The EMBO journal · 2026Review
- Combining QTL mapping and RNA-Seq reveals candidate genes controlling flag leaf width in foxtail millet.BMC plant biology · 2025Article
- Design and Expression ofInternational journal of molecular sciences · 2025Article
- Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.Genome research · 2024Article
- Shaping rice Green Revolution traits by engineering ATG immediate upstream 5'-UTR sequences of OsSBI and OsHTD1.Plant biotechnology journal · 2024Article
- Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task.PLoS computational biology · 2023Article
- Article
- Tandem repeats ubiquitously flank and contribute to translation initiation sites.BMC genomic data · 2022Article
- The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation.RNA (New York, N.Y.) · 2022Article
- Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation.Cell systems · 2022Article
- Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data.Nucleic acids research · 2022Article
- Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis.Frontiers in plant science · 2022Article
- Widespread translational control regulates retinal development in mouse.Nucleic acids research · 2021Article
- Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed.Nucleic acids research · 2021Article
- Control of translation by eukaryotic mRNA transcript leaders-Insights from high-throughput assays and computational modeling.Wiley interdisciplinary reviews. RNA · 2021Review
- A translation enhancer element from black beetle virus engages yeast eIF4G1 to drive cap-independent translation initiation.Scientific reports · 2021Article
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
- Inferring efficiency of translation initiation and elongation from ribosome profiling.Nucleic acids research · 2020Article
- So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes.EMBO reports · 2020Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundGeneral translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate to control translation rates are not well understood.
resultsHere, we show that these sequence features specify 42-81% of the variance in translation rates in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Mus musculus, and Homo sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25-60 nucleotide segments within mRNA 5' regions, that changes in tri-nucleotide frequencies between highly and poorly translated 5' regions are correlated between all species, and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA.
conclusionsOur work shows that general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that directs translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and within cis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell.
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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.