Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Alternative splicing (AS) significantly increases transcript diversity in higher eukaryotes.
• Studies suggest 60-80% of human genes undergo alternative splicing.
• Understanding AS variation across species is crucial for deciphering genomic complexity.

Purpose of the Study:

• To analyze and quantify alternative splicing patterns in chicken, human, and mouse.
• To compare transcript diversity and AS complexity across these three species.
• To classify splicing patterns based on distinct and variant exon usage.

Main Methods:

• A splicing pattern approach was employed for bioinformatics analysis.
• Exons were categorized into distinct and variant types.
• Four permutation classes (I-IV) were defined to classify splicing patterns.
• Comparative genome analysis focused on orthologous genes.

Main Results:

• 23% of chicken genes are alternatively spliced, compared to 68% in humans and 57% in mice.
• Chicken genes show fewer AS events but similar AS event percentages, indicating higher transcript diversity per gene.
• Chicken genes have fewer transcripts per gene and shorter introns than human and mouse genes.

Conclusions:

• Chicken genes predominantly produce 2-3 isoforms, while human and mouse genes produce ~8 and ~6, respectively.
• Intron definition is more prominent in chicken than exon definition, evidenced by higher intron retention.
• Variant exon splicing patterns reveal species-specific differences in alternative transcript diversity.