Exonic splice regulation imposes strong selection at synonymous sites.

Area of Science:

• Genetics
• Molecular Biology
• Evolutionary Biology

Background:

• Exonic splice regulatory signals are vital for gene expression, but their precise contribution to coding sequence evolution remains unclear.
• Previous studies have not differentiated the prevalence of splice regulatory elements from the strength of evolutionary constraints acting upon them.
• Existing data support scenarios ranging from weak, diffuse constraint to strong purifying selection in specific sequence pockets.

Purpose of the Study:

• To quantify the proportion of coding nucleotides involved in splicing.
• To determine the strength of evolutionary selection maintaining these splicing-related nucleotides.
• To distinguish between weak, diffuse constraint and strong purifying selection on exonic splice enhancers (ESEs).

Main Methods:

• Utilized multiple analytical methods to assess the distribution of selection coefficients for new mutations within ESEs.
• Analyzed evolutionary constraint on functional ESEs within coding sequences.
• Investigated the impact of mutations disrupting ESEs on fitness and potential clinical relevance.

Main Results:

• Convergent analyses suggest that approximately 15%-20% of fourfold degenerate sites are part of functional ESEs.
• The majority of these functional ESE sites are under strong evolutionary constraint.
• This indicates that exonic splice regulation is a potent force, significantly constraining the evolution of a substantial fraction of coding nucleotides.

Conclusions:

• Exonic splice enhancers (ESEs) are not merely weak modifiers of codon usage bias but are under strong selective pressure.
• A significant proportion of coding sequence nucleotides are constrained by selection to maintain splicing fidelity.
• Synonymous mutations disrupting ESEs represent a potentially common cause of single-locus genetic disorders.