Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution

Area of Science:

• Molecular Biology
• Genetics
• Evolutionary Biology

Background:

• Exonic sequences contain regulatory splicing elements that overlap with coding capacity.
• Genomic variability studies often overlook the impact of synonymous variations on splicing efficiency.
• Synonymous variations are typically considered functionally neutral in clinical genetics and molecular evolution.

Purpose of the Study:

• To analyze the evolutionary conflict between splicing efficiency and coding capacity.
• To investigate the functional impact of synonymous variations on RNA splicing.
• To evaluate the role of splicing control in evolutionary selection.

Main Methods:

• Utilized cystic fibrosis transmembrane conductance regulator (CFTR) exon 12 splicing as a model system.
• Assessed the effect of synonymous variations on exon skipping.
• Performed comparative splicing evaluation of mammalian sequence divergences.

Main Results:

• Approximately 25% of synonymous variations in CFTR exon 12 led to exon skipping and inactive CFTR protein.
• Artificial combinations of CFTR exon 12 synonymous and nonsynonymous substitutions demonstrated incompatibility with normal RNA processing.
• A combination of mouse synonymous and human missense variations in CFTR exon 12 induced exon skipping.

Conclusions:

• Synonymous variations are not always functionally neutral and can significantly impact splicing efficiency.
• Evolutionary selection operates at two sequential levels: splicing control and protein function optimization.
• Findings necessitate a re-evaluation of synonymous variations in clinical genetics and evolutionary studies.