Using protein-per-mRNA differences among human tissues in codon optimization.

ABSTRACT:

Background

Codon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized that different tissues have distinct tRNA profiles and codon usages in their transcriptomes, the effect of tissue-specific codon optimality on protein synthesis remains elusive.

Results

We leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enriched or depleted in specific tissues. We detect two clusters of tissues with an opposite pattern of codon preferences. We then use these identified patte

SUBMITTER: Hernandez-Alias X 

PROVIDER: S-EPMC9951436 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature