Alternative splicing generates transcript variants from over 90% of human genes and its disruption causes or contributes to numerous diseases and disorders. We have discovered a highly conserved AS regulatory network comprising a few hundred 3–27 nucleotide-long neuronal ‘microexons’ and a master activator of these exons, the neuronal-specific Ser/Arg-repeat protein nSR100/SRRM4. Remarkably, this network is disrupted in approximately one-third of analyzed human subjects diagnosed with autism spectrum disorder (ASD). Furthermore, we have observed that: (1) neuronal microexons are enriched in genes with critical functions associated with neurogenesis and synaptic biology, as well as genetic variants linked to ASD; (2) ~200 hundred genes impact microexon regulation and these are also enriched in ASD-linked variants; and (3) mice haploinsufficient for SRRM4 or harboring deletions of individual microexons display hallmark ASD-like phenotypes. Collectively, these studies provide evidence that a neuronal microexon network represents a regulatory ‘hub’ commonly impacted — and causally implicated — in autism. However, the full landscape of neuronal microexons as well as the molecular and genetic mechanisms directly resulting in their disruption are not known. Moreover, the function of the vast majority of microexons, including those disrupted in ASD, are also unknown.
To address these questions, we are integrating machine learning, extensive bulk and single cell transcriptome profiling, and new functional genomic strategies to discover and characterize microexons. These approaches have delineated several hundred new examples, many of which display neuronal subtype-specific splicing patterns. Through elucidation of a microexon ‘recognition code’ we have systematically delineated cis-regulatory elements and ASD-linked variants that directly impact their splicing. Finally, using a dual CRISPR-Cas editing system we are systematically investigating functions of microexons, as well as of alternative splicing events belonging to other critical regulatory programs. Recent progress in these areas will be presented.