Bichromatic exon-reporters reveal voltage-gated Ca2+-channel splice-isoform diversity across Drosophila neurons in vivo

Every neuron contains the same genomic information but its complement of proteins is the product of countless neuron-specific steps including pre-mRNA splicing. Despite advances in RNA sequencing techniques, pre-mRNA splicing biases that favor one isoform over another are largely inscrutable in live neurons in situ. Here, in Drosophila, we developed bichromatic fluorescent reporters to investigate alternate splicing of cacophony - a gene that codes the pore-forming 1-subunit of the primary neuronal voltage-gated Ca2+ channel (VGCC). These reporters reveal a neuron-specific pattern of exon biases, including stereotypical differences between neurons of the same neurotransmitter type and ostensibly the same function. Information about exon splicing biases of individual neurons in vivo provides clues to the role of VGCC motifs and the role of those neurons in the context of local circuits. The application of this technology to a large gene such as cacophony provides a precedence for effective exon-reporter design for other Drosophila genes.