Codon usage bias in health and in aging: is this a problem?

• Main Author: Almeida, Francisca Gomes
• Publication Date: 2023
• Format: Master thesis
• Language: eng
• Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
• Download full: http://hdl.handle.net/10773/40952
• topic: Codon; Transcription; Codon usage bias; Time points; Aging; Expression; Python; Genes

Codon usage bias, a phenomenon involving the preferential usage of specific synonymous codons over others, plays a pivotal role in molecular biology. This bias is intimately associated with the process of translation and its complex relationship to the expression of genes. Genomic GC content, tRNA availability, gene expression levels, and environmental influences are some of the major causes of codon usage bias. These variables interact dynamically to produce intricate patterns of codon preferences that affect different aspects of functional dynamics and cellular adaptability. The effects of bias in codon usage are extensive. It affects, for example, protein-protein interactions, protein stability and folding and also cellular functions, mRNA stability and decay along with the efficiency of protein synthesis and gene expression regulation. This project aimed to develop a Python pipeline for analysing codon usage bias in Escherichia coli and Mus musculus transcriptomes. The pipeline facilitated in-depth analysis of codon usage patterns throughout several life stages by comparing codon counts, RSCU, CAI values. To find significant differences, a variety of data visualization and gene expression comparison tools were used in conjunction with statistical testing. The utilization of codons in the liver and brain tissues of Mus musculus was shown to be remarkably stable throughout time. Gene expression changes during development were mirrored in differences in individual amino acids at different time intervals, although overall codon patterns remained stable. Analysing codon usage differences in differential expressed genes only allowed showing how gene translation mechanisms are flexible in response to age, gender, and other stimuli. In-depth investigation is required to fully comprehend the intricate dynamics of codon usage in aging.