Widespread alternative and aberrant splicing revealed by lariat sequencing

Area of Science:

• Molecular Biology
• Genomics
• Eukaryotic Gene Regulation

Background:

• Alternative splicing is a key eukaryotic gene feature driving proteome diversity.
• Fission yeast (Schizosaccharomyces pombe) offers a simple model with mammalian-like splice site features.
• Previous estimates underestimated the prevalence and frequency of alternative splicing events.

Purpose of the Study:

• To comprehensively profile splicing events in Schizosaccharomyces pombe using intron lariat sequencing.
• To quantify the extent and frequency of alternative splicing, including novel events.
• To investigate the conservation and regulation of alternative splicing.

Main Methods:

• Intron lariat sequencing to capture splicing intermediates.
• Analysis of splicing events in Schizosaccharomyces pombe.
• Validation of splicing events using RNA sequencing (RNAseq).

Main Results:

• Discovered extensive alternative splicing, affecting over 50% of annotated introns.
• Identified hundreds of novel exon-skipping events and thousands of new introns.
• Alternative splice sites occur at ~3% the rate of canonical sites, with higher rates in lowly expressed genes.
• Lariat sequencing revealed significantly more alternative splicing than RNAseq, likely due to transcript decay.

Conclusions:

• The spliceosome exhibits lower fidelity than previously appreciated.
• Alternative splicing significantly contributes to generating novel gene structures.
• Most identified alternative splicing events lack detectable conservation, suggesting potential roles beyond conserved functions.