Cataloging the potential functional diversity of Cacna1e splice variants using long-read sequencing

Area of Science:

• Neuroscience
• Molecular Biology
• Genomics

Background:

• Alternative RNA splicing's impact on voltage-gated calcium channel (VGCC) function and structure is not well understood.
• The Cacna1e (Cav2.3) gene encodes a VGCC subunit, and its splice variants are crucial for neuronal function.

Purpose of the Study:

• To catalog rat Cacna1e splice variants using long-read RNA sequencing.
• To computationally prioritize splice variants with the potential to impact channel function.
• To establish a strategy for evaluating splice variant function in ion channels.

Main Methods:

• Long-read RNA sequencing (Oxford Nanopore) of rat thalamus.
• Computational analysis of Cacna1e transcripts to predict amino acid sequences and identify splicing events.
• Prioritization of splice variants based on expression and conservation.

Main Results:

• Sequenced 2,110 unique Cacna1e splice variants from rat thalamus.
• Identified up to 154 variants with the potential to encode a functional channel.
• Discovered 31 cassette splicing events affecting channel function, with three exons highly expressed and conserved.

Conclusions:

• This study provides the first long-read sequencing data for Cacna1e.
• Offers the first computational evaluation of Cacna1e splice variants.
• The developed strategy can be applied to understand splice variant function across various ion channel types and their role in disease.