Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA.
High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA.
J Mol Biol. 2020 May 15;432(11):3369-3378. doi: 10.1016/j.jmb.2020.01.011. Epub 2020 Jan 23.
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.
多细胞生物中的蛋白质表达在组织间广泛变化。每个组织中转录组中的密码子使用情况源自基因组密码子使用情况和每个基因的相对表达水平。我们创建了一个全面的计算资源，其中包含了 51 个人类组织（TissueCoCoPUTs：https://hive.biochemistry.gwu.edu/review/tissue_codon）的组织特异性密码子、密码子对和二核苷酸使用数据，这些数据来自 Broad Institute Genotype-Tissue Expression (GTEx) 门户的转录组数据。组织特异性密码子和密码子对频率之间的距离用于生成一个基于每个组织中独特的密码子和密码子对使用模式的系统发育树，这些模式与基因组分布明显不同。这个新资源可能有助于揭示密码子使用与 tRNA 丰度之间的关系，这对于确定跨组织的翻译动力学和效率可能至关重要。生物治疗开发、组织特异性基因工程和遗传疾病预测等研究领域将极大地受益于这个资源。
