Complexity and graded regulation of neuronal cell-type–specific alternative splicing revealed by single-cell RNA sequencing

Significance Alternative splicing (AS) is extensively used in the mammalian brain, but its contribution to the molecular and cellular diversity across neuronal cell types remains poorly understood. Through systematic and integrative analysis of over 100 transcriptomically defined cortical neuronal types, we found neuronal subclass-specific splicing-regulatory programs consist of overlapping alternative exons showing differential splicing at multiple hierarchical levels. Evidence is provided that this graded AS regulation is controlled by unique combinations of RNA-binding proteins (RBPs). Importantly, these RBPs also contribute to splicing dynamics across neuronal cell types that do not conform to the hierarchical taxonomy established based on transcriptional profiles, suggesting that the graded AS regulation may provide a molecular mechanism orthogonal to transcriptional regulation in specifying neuronal identity and function.