junctionCounts: comprehensive alternative splicing analysis and prediction of isoform-level impacts to the coding...

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Alternative splicing (AS) is a key regulator of complex biological processes.
• Current transcriptomic studies often identify AS events but lack tools to predict their functional consequences.
• Existing tools for AS event prediction have significant limitations.

Purpose of the Study:

• To develop novel computational tools for quantifying AS events and predicting their functional impact on coding sequences.
• To address the unmet need for predicting the functional consequences of alternative splicing changes.
• To provide a robust method for analyzing splicing dynamics and mRNA isoform fate.

Main Methods:

• Development of junctionCounts for quantifying simple and complex pairwise AS events using RNA-seq junction reads.
• Implementation of cdsInsertion for identifying coding sequence (CDS) information and premature termination codons via in silico translation.
• Creation of findSwitchEvents to link AS events with CDS data for predicting isoform-level CDS impact.
• Application of the developed tools to characterize splicing dynamics and NMD regulation during primate neuronal differentiation.

Main Results:

• junctionCounts demonstrates competitive sensitivity, false discovery rate, and quantification accuracy compared to similar tools.
• The developed pipeline effectively captures both simple and complex AS events.
• Analysis of primate neuronal differentiation revealed insights into splicing dynamics and NMD regulation.

Conclusions:

• junctionCounts and its associated utilities provide a robust framework for analyzing alternative splicing events and predicting their functional outcomes.
• The tools are capable of characterizing AS in diverse organisms and predicting effects on mRNA isoform fate.
• This work advances the ability to understand the functional implications of alternative splicing in biological regulation.