Differentiated evolutionary rates in alternative exons and the implications for splicing regulation

Area of Science:

• Evolutionary biology
• Molecular biology
• Genomics

Background:

• Alternative splicing diversifies gene function through regulated exon inclusion.
• Conserved motifs in exons and introns govern alternative splicing.
• Conflicting data exists on sequence conservation and substitution rates in alternative exons.

Purpose of the Study:

• To analyze the evolution of alternative and constitutive exons in mammals.
• To investigate the role of exonic structure conservation in exon evolution.
• To define and apply a measure of exonic splicing enhancer (ESE) arrangement conservation.

Main Methods:

• Comparative analysis of human and mouse protein-coding exons.
• Assessment of transcript exonic structure conservation.
• Calculation of synonymous (dS) and non-synonymous (dN) substitution rates.
• Definition and application of an ESE-conservation score.

Main Results:

• Lack of exonic structure conservation correlates with relaxed evolutionary constraints (higher dS and dN).
• Alternative exons in non-conserved structures exhibit the least sequence constraint.
• Constitutive exons show higher ESE arrangement conservation than alternative exons.
• Flanking intron conservation increases for alternative exons with high ESE conservation.

Conclusions:

• Transcript exonic structure conservation explains most dN differences between alternative and constitutive exons.
• Low dS values are specific to alternative exons with conserved structures.
• High ESE arrangement conservation in constitutive exons and conserved alternative exons suggests regulatory roles for flanking introns.