Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia

Abstract

BACKGROUND: Alternative splicing contributes to molecular diversity across brain cell types. RNA-binding proteins (RBPs) regulate splicing, but the genome-wide mechanisms underlying cell-type-specific splicing remain poorly understood. RESULTS: Here, we want to unravel cell-type-specific splicing mechanisms by using 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 the human hippocampus and frontal cortex. We found that exon inclusion of variable exons 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, we accurately predict and prioritize the effect of splicing QTLs. CONCLUSIONS: Our results indicate that the splicing mechanisms in variable exons in neurons diverged more from the standard mechanisms. Splicing in neurons might be less sequence-dependent and influenced more by, for instance, chromatin accessibility or methylation. Taken together, these results highlight new insights into the mechanisms regulating cell-type-specific alternative splicing in the brain.