ArticleGenome biology and evolution2012
Weak 5'-mRNA secondary structures in short eukaryotic genes.
Article in Genome biology and evolution, 2012. 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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Who cites it
18 citing papers in PubMed.
- UTR-DynaPro: a CNN-transformer multimodal language model for decoding 5'UTR regulatory mechanisms.Scientific reports · 2026Article
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- Native functions of short tandem repeats.eLife · 2023Article
- Rational design and construction of multi-copy biomanufacturing islands in mammalian cells.Nucleic acids research · 2022Article
- Review
- So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes.EMBO reports · 2020Review
- eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide.RNA (New York, N.Y.) · 2020Article
- Pervasive and dynamic transcription initiation inGenome research · 2019Article
- Article
- Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Ribosome reinitiation can explain length-dependent translation of messenger RNA.PLoS computational biology · 2017Article
- eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation.Cell reports · 2016Article
- Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.Molecular systems biology · 2014Article
- Translational control of gene expression in the gonadotrope.Molecular and cellular endocrinology · 2014Review
- Article
- Efficient translation initiation dictates codon usage at gene start.Molecular systems biology · 2013Article
- Single nucleotide polymorphisms of CD20 gene and their relationship with clinical efficacy of R-CHOP in patients with diffuse large B cell lymphoma.Cancer cell international · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Experimental studies of translation have found that short genes tend to exhibit greater densities of ribosomes than long genes in eukaryotic species. It remains an open question whether the elevated ribosome density on short genes is due to faster initiation or slower elongation dynamics. Here, we address this question computationally using 5'-mRNA folding energy as a proxy for translation initiation rates and codon bias as a proxy for elongation rates. We report a significant trend toward reduced 5'-secondary structure in shorter coding sequences, suggesting that short genes initiate faster during translation. We also find a trend toward higher 5'-codon bias in short genes, suggesting that short genes elongate faster than long genes. Both of these trends hold across a diverse set of eukaryotic taxa. Thus, the elevated ribosome density on short eukaryotic genes is likely caused by differential rates of initiation, rather than differential rates of elongation.
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