iCodon

iCodon predicts and manipulates mRNA stability by optimizing codon composition to modulate steady-state gene expression.

Key Features:

• Synonymous codon substitution: Introduces synonymous codon substitutions into coding sequences to alter codon composition.
• mRNA stability prediction: Predicts mRNA stability based on specific codon compositions and codon optimality.
• Optimization and deoptimization: Generates more stable (optimized) or less stable (deoptimized) mRNA variants that encode identical proteins.
• Species-specific transcriptomes: Optimized for four vertebrate transcriptomes: mouse, human, frog, and fish.
• Translation-dependent mechanism: Accounts for codon optimality operating in a translation-dependent manner across species.
• Empirical validation correlation: Predictive capabilities correlate with expression in fluorescent reporter assays and endogenous genes in human cells and zebrafish embryos.
• Link to steady-state expression: Explicitly links codon composition and mRNA stability to steady-state gene expression levels.

Scientific Applications:

• Gene expression tuning: Fine-tunes gene expression levels in experimental constructs by modulating mRNA stability via codon choice.
• Comparative transcriptomics: Studies codon optimality and translation-dependent effects across vertebrate species (mouse, human, frog, fish).
• Reporter and endogenous analysis: Designs and interprets fluorescent reporter assays and analyzes endogenous gene expression in human cells and zebrafish embryos.
• Biotechnology and therapeutics: Supports design of genetic constructs for biotechnological applications, therapeutic purposes, and vaccine development by controlling mRNA stability.

Methodology:

Introduces synonymous codon substitutions and predicts mRNA stability from codon composition using species-specific optimizations for mouse, human, frog, and fish transcriptomes.