TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression. Issue 11 (15th May 2020)

• Record Type: Journal Article
• Authors: Kames, Jacob; Alexaki, Aikaterini; Holcomb, David D.; Santana-Quintero, Luis V.; Athey, John C.; Hamasaki-Katagiri, Nobuko; Katneni, Upendra; Golikov, Anton; Ibla, Juan C.; Bar, Haim; Kimchi-Sarfaty, Chava
• Is Part Of: Journal of molecular biology. Volume 432:Issue 11(2020)
• Page Start: 3369
• Page End: 3378
• Publication Date: 2020-05-15
• Subjects: transcriptome -- GTEx -- tRNA -- genetic engineering -- Homo sapiens; TissueCoCoPUTs tissue Codon and Codon Pair Usage Tables -- CoCoPUTs codon and codon-pair usage tables -- GTEx genotype-Tissue Expression -- HIVE high-performance integrated virtual environment -- ENc effective number of codons -- ENcp effective number of codon-pairs -- MDS multidimensional scaling -- CDSs coding sequences -- TPM transcripts per million -- ENST ensembl spliced transcript -- GC guanine-cytosine; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2020.01.011
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: Protein expression in multicellular organisms varies widely across tissues. Codon usage in the transcriptome of each tissue is derived from genomic codon usage and the relative expression level of each gene. We created a comprehensive computational resource that houses tissue-specific codon, codon-pair, and dinucleotide usage data for 51 Homo sapiens tissues (TissueCoCoPUTs: https://hive.biochemistry.gwu.edu/review/tissue_codon), using transcriptome data from the Broad Institute Genotype-Tissue Expression (GTEx) portal. Distances between tissue-specific codon and codon-pair frequencies were used to generate a dendrogram based on the unique patterns of codon and codon-pair usage in each tissue that are clearly distinct from the genomic distribution. This novel resource may be useful in unraveling the relationship between codon usage and tRNA abundance, which could be critical in determining translation kinetics and efficiency across tissues. Areas of investigation such as biotherapeutic development, tissue-specific genetic engineering, and genetic disease prediction will greatly benefit from this resource. Graphical abstract: Image 1 Highlights: New database based on tissue-specific GTEx transcriptomic data for 51 Homo sapiens tissues. User-friendly interface visualizing codon, codon-pair, and dinucleotide data. TissueCoCoPUTs can be used in predicting translation efficiency and kinetics. TissueCoCoPUTs can be used for tissue-targeted recombinant therapeutics or gene therapy design and optimization. TissueCoCoPUTs may facilitate the development of genetic disease prediction tools.