Exon size and sequence conservation improves identification of splice-altering nucleotides

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Genomics

Background:

• Pre-messenger RNA (pre-mRNA) splicing is orchestrated by trans-acting splicing factors binding to pre-mRNA.
• Exon evolution is influenced by both coding and splicing selective pressures.
• Previous studies suggest comparing exons of identical size aids in deconvoluting splicing pressures.

Purpose of the Study:

• To test if exon size-filtered sequence alignments enhance the identification of nucleotides involved in efficient exon ligation.
• To investigate the relationship between exon size conservation, sequence conservation, and alternative splicing.
• To determine if exon size-filtered comparisons improve the detection of splice-altering nucleotides, particularly in disease-associated exonic single nucleotide polymorphisms (SNPs).

Main Methods:

• Creation of an exon size database by filtering 76 vertebrate sequence alignments based on conserved exon size.
• Analysis of genomic parameters including splice-site strength, gene position, and flanking intron length.
• Examination of a dataset of approximately 5000 exonic SNPs associated with disease.

Main Results:

• Highly size-conserved exons are consistently sequence-conserved, but sequence conservation does not guarantee size conservation.
• Exon length conservation strongly predicts alternative splicing, particularly for evolutionarily young exons.
• Exon size-filtered alignments improve splice predictions for mutations at the third codon position, especially those reducing exon inclusion efficiency, and identify splice-altering nucleotides at wobble positions.

Conclusions:

• Coding pressures are dominant at invariable codon positions.
• Exon size-filtered sequence alignments are effective in identifying splice-altering nucleotides at wobble positions.
• Length conservation serves as a key indicator for alternative splicing and aids in understanding nucleotide evolution in exons.