Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals

Neurons draw on alternative splicing for their increased transcriptomic complexity throughout animal phylogeny. To delve into the mechanisms controlling the assembly and evolution of this regulatory layer, we characterized the neuronal microexon program in Drosophila and compared it with that of mammals. In Drosophila, alternative splicing profiling across tissues and neuronal types show pan-neuronal expression of this program with some variation in photoreceptors and Kenyon cells. This neuronal specificity is driven by the enhancer of microexons (eMIC) domain of Srrm234, which is expressed in neurons through post-transcriptional processing at the 3' end of the gene by the RNA binding proteins embryonic lethal abnormal vision (Elav) and found in neurons (Fne). Both loss-of-function and misexpression of the eMIC domain lead to widespread neurological alterations associated with the skipping of short neural exons, revealing a tight regulation of this AS program in neurons. These defects emerge largely from alterations in neuronal activity, as revealed by a combination of neuronal imaging experiments and cell-type-specific rescues and in line with a strong enrichment for ion channels among genes with eMIC-dependent exons. Remarkably, we found minimal overlap of eMIC regulated exons between flies and mice, illustrating how ancient post-transcriptional programs can evolve independently in different phyla to impact distinct cellular modules while maintaining cell-type specificity.