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TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression.

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.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Kames J,Alexaki A,Holcomb DD,Santana-Quintero LV,Athey JC,Hamasaki-Katagiri N,Katneni U,Golikov A,Ibla JC,Bar H,Kimchi-Sarfaty C

doi

10.1016/j.jmb.2020.01.011

subject

Has Abstract

pub_date

2020-05-15 00:00:00

pages

3369-3378

issue

11

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(20)30041-3

journal_volume

432

pub_type

杂志文章

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