CUBAP: an interactive web portal for analyzing codon usage biases across populations

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Synonymous codon usage influences gene expression, mRNA/protein structure, and disease.
• Population-specific codon usage biases are understudied.
• Understanding these biases is crucial for interpreting genetic variations.

Purpose of the Study:

• To develop a web server (CUBAP) for analyzing population-specific codon usage biases.
• To investigate differences in codon usage across diverse populations.
• To explore the implications of these biases for gene function and disease association.

Main Methods:

• Utilized the 1000 Genomes Project data for 17,634 genes.
• Calculated and visualized population-specific codon frequencies, codon aversion, codon pairing, ramp sequences, and nucleotide composition.
• Developed the CUBAP web server (https://cubap.byu.edu) for comprehensive analysis.

Main Results:

• Identified significant population-specific differences in codon pairing for 35.8% of genes.
• Achieved high accuracy (98.8% African, 100% East Asian) in predicting individuals' origins based on codon pairing.
• Discovered a decreased CTG pairing bias in the IRGM gene in East Asian and African populations, potentially affecting Crohn's disease association.

Conclusions:

• CUBAP provides a valuable tool for analyzing population-specific codon usage biases.
• Codon pairing variations can serve as markers for population origin.
• Synonymous codon usage differences have functional implications for gene expression and disease susceptibility across populations.