RNA splicing is a key mechanism linking genetic variation and complex diseases, including schizophrenia. Splicing profiles are particularly diverse in the brain, but it can be difficult to accurately identify and quantify full-length mRNA isoforms using standard approaches, impeding the identification of splice isoforms linked to disease. Emblematic of this is CACNA1C, a large gene that shows robust genetic associations with several psychiatric disorders and encodes multiple, functionally-distinct, voltage-gated calcium channels via alternative splicing. However, the extreme length (>13kb), number of exons (>50) and high level of alternative splicing means CACNA1C isoform structure and expression is poorly understood.
We have investigated CACNA1C expression in six regions of post-mortem human brain by long-read Nanopore sequencing of the complete coding sequence from expressed transcripts. The ability of Nanopore sequencing to define the complete exonic structure of CACNA1C transcripts allows us to identify known and novel gene isoforms, including novel exons, microexons and multi-exonic skipping events and their expression across multiple brain regions. We show that the CACNA1C splice isoform profile varies between brain regions and is substantially more complex than currently appreciated: we identified 34 novel exons and 83 high confidence novel transcripts, a number of which are abundantly expressed and predicted to alter protein function. Our findings demonstrate that knowledge of human splice isoform diversity remains far from complete. Furthermore, the accurate characterisation of CACNA1C isoforms with long-read sequencing will now facilitate the identification of disease-linked isoforms and future studies on CACNA1C’s role in psychiatric disorders.