ArticleNucleic acids research2010
Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Mechanisms of and mitigating strategies for cellular immune responses to CRISPR-associated nucleases in genome editing therapy.Frontiers in medicine · 2026Review
- Translation elongation: measurements and applications.RNA biology · 2025Review
- Deep generative optimization of mRNA codon sequences for enhanced mRNA translation and therapeutic efficacy.Nature communications · 2025Article
- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Ramp Sequence May Explain Synonymous Variant Association with Alzheimer's Disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA).Biomedicines · 2025Article
- Ramp sequence may explain synonymous variant association with Alzheimer's disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (bioRxiv : the preprint server for biology · 2025Article
- A generative framework for enhanced cell-type specificity in rationally designed mRNAs.bioRxiv : the preprint server for biology · 2024Article
- Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues.Genomics, proteomics & bioinformatics · 2023Article
- Human Tissues Exhibit Diverse Composition of Translation Machinery.International journal of molecular sciences · 2023Article
- Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice.Plant communications · 2023Article
- AAV vectors: The Rubik's cube of human gene therapy.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Review
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- Synonymous mutations in the phosphoglycerate kinase 1 gene induce an altered response to protein misfolding inFrontiers in microbiology · 2022Article
- CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern.Protein science : a publication of the Protein Society · 2022Article
- Codon optimality in cancer.Oncogene · 2021Review
- CAMAP: Artificial neural networks unveil the role of codon arrangement in modulating MHC-I peptides presentation.PLoS computational biology · 2021Article
- High-throughput interrogation of programmed ribosomal frameshifting in human cells.Nature communications · 2020Article
- Translational efficiency across healthy and tumor tissues is proliferation-related.Molecular systems biology · 2020Article
- The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain.Scientific reports · 2018Article
- Exonic splice regulation imposes strong selection at synonymous sites.Genome research · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Various studies in unicellular and multicellular organisms have shown that codon bias plays a significant role in translation efficiency (TE) by co-adaptation to the tRNA pool. Yet, in humans and other mammals the role of codon bias is still an open question, with contradictory results from different studies. Here we address this question, performing a large-scale tissue-specific analysis of TE in humans, using the tRNA Adaptation Index (tAI) as a direct measure for TE. We find tAI to significantly correlate with expression levels both in tissue-specific and in global expression measures, testifying to the TE of human tissues. Interestingly, we find significantly higher correlations in adult tissues as opposed to fetal tissues, suggesting that the tRNA pool is more adjusted to the adult period. Optimization based analysis suggests that the tRNA pool-codon bias co-adaptation is globally (and not tissue-specific) driven. Additionally, we find that tAI correlates with several measures related to the protein functionally importance, including gene essentiality. Using inferred tissue-specific tRNA pools lead to similar results and shows that tissue-specific genes are more adapted to their tRNA pool than other genes and that related sets of functional gene groups are translated efficiently in each tissue. Similar results are obtained for other mammals. Taken together, these results demonstrate the role of codon bias in TE in humans, and pave the way for future studies of tissue-specific TE in multicellular organisms.
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