RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae

Area of Science:

• Molecular Biology
• Genetics
• Bioinformatics

Background:

• Alternative splicing generates mRNA diversity by varying exon combinations.
• Saccharomyces cerevisiae (yeast) possess regulatory factors distinct from metazoans, suggesting limited alternative splicing.
• Recent evidence indicates functional alternative splicing in yeast, particularly under environmental stress.

Purpose of the Study:

• To develop a computational classifier for predicting 3' splice sites (ss) in Saccharomyces cerevisiae.
• To investigate the role of pre-mRNA sequence and structure in alternative 3'ss selection.
• To explore the impact of environmental factors, such as temperature, on alternative splicing in yeast.

Main Methods:

• Computational classification using sequence and structure properties of pre-mRNA.
• Experimental validation of predicted alternative 3' splice sites.
• Genome-wide analysis of temperature effects on splicing.

Main Results:

• A computational model accurately predicts most annotated 3'ss in yeast CDS and 5' UTR.
• The same rules govern the selection of alternative 3'ss, though their usage is low.
• Many alternative 3'ss lead to premature termination codons (PTCs), implying a regulatory role.
• Temperature-induced splicing changes are minimal, suggesting limited widespread regulation.

Conclusions:

• Alternative 3'ss selection in yeast is mediated by pre-mRNA structure.
• This splicing mechanism may be responsive to external cues like temperature.
• Alternative splicing in yeast is likely involved in gene expression control, potentially via PTCs.