RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse in brain and difficult to accurately identify and quantify. We developed a new approach to address this challenge, combining long-range PCR and nanopore sequencing with a novel bioinformatics pipeline. We identify the full-length coding transcripts of CACNA1C in human brain. CACNA1C is a psychiatric risk gene that encodes the voltage-gated calcium channel Ca V 1.2. We show that CACNA1C's transcript profile is substantially more complex than appreciated, identifying 38 novel exons and 241 novel transcripts. Importantly, many of the novel variants are abundant, and predicted to encode channels with altered function. The splicing profile varies between brain regions, especially in cerebellum. We demonstrate that human transcript diversity (and thereby protein isoform diversity) remains undercharacterised, and provide a feasible and cost-effective methodology to address this. A detailed understanding of isoform diversity will be essential for the translation of psychiatric genomic findings into pathophysiological insights and novel psychopharmacological targets.

RNA splicing is a key mechanism linking genetic variation and complex diseases, including schizophrenia. Splicing profiles are particularly diverse in the brain, but it is difficult to accurately identify and quantify full-length isoforms using standard approaches. CACNA1C is a large gene that shows robust genetic associations with several psychiatric disorders and encodes multiple, functionally-distinct voltage-gated calcium channels via alternative splicing. We combined long-range PCR with nanopore sequencing to characterise the full-length coding sequences of the CACNA1C gene in human brain. We show that its splice isoform profile varies between brain regions and is substantially more complex than currently appreciated: we identified 38 novel exons and 83 high confidence novel isoforms, many of which are predicted to alter protein function. Our findings demonstrate the capability of long-read amplicon sequencing to effectively characterise human splice isoform diversity, while the accurate characterisation of CACNA1C isoforms will facilitate the identification of disease-linked isoforms.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

No abstract