Predicting cell-type-specific exon inclusion in the human brain reveals more complex splicing mechanisms in neurons than glia

Abstract

Alternative splicing contributes to molecular diversity across brain cell types. RNA-binding proteins (RBPs) regulate splicing, but the genome-wide mechanisms remain poorly understood. Here, we used RBP binding sites and/or the genomic sequence to predict exon inclusion in neurons and glia as measured by long-read single-cell data in human hippocampus and frontal cortex. We found that alternative splicing is harder to predict in neurons compared to glia in both brain regions. Comparing neurons and glia, the position of RBP binding sites in alternatively spliced exons in neurons differ more from non-variable exons indicating distinct splicing mechanisms. Model interpretation pinpointed RBPs, including QKI, potentially regulating alternative splicing between neurons and glia. Finally, using our models, we accurately predict and prioritize the effect of splicing QTLs. Taken together, our models provide new insights into the mechanisms regulating cell-type-specific alternative splicing and can accurately predict the effect of genetic variants on splicing.