Coordinated alternative splicing decisions via stepwise exon definition

Area of Science:

• Molecular Biology
• Genetics
• Computational Biology

Background:

• Alternative splicing of pre-messenger RNA (mRNA) is crucial for gene regulation in humans.
• Aberrant splicing, including alternative exon (AE) skipping/inclusion and intron retention (IR), is linked to diseases like cancer.
• The spliceosome orchestrates splicing, but its coordination of diverse splicing decisions remains unclear.

Purpose of the Study:

• To investigate the coordination between alternative exon inclusion and intron retention.
• To elucidate the molecular mechanisms underlying the regulation of these splicing events.
• To explore the role of spliceosome dynamics in cancer-associated splicing deregulation.

Main Methods:

• Analysis of large-scale mutagenesis screening data.
• Transcriptome-wide RNA sequencing (RNA-seq) for splicing analysis.
• Data-driven mathematical modeling of spliceosome assembly and function.

Main Results:

• Intron retention adjacent to alternative exons frequently occurs at intermediate inclusion levels.
• Multistep exon recognition, driven by spliceosome assembly, explains the dependency between AE inclusion and IR.
• This multistep recognition is perturbed in cancer cells, leading to coordinated splicing deregulation.

Conclusions:

• Stepwise alternative exon recognition by the spliceosome coordinates AE inclusion and flanking intron retention.
• This mechanism provides insights into how spliceosome dynamics regulate splicing decisions.
• Understanding these coordinated events may reveal common molecular mechanisms underlying splicing errors in cancer.