Alternative splicing in layer 3 pyramidal neurons differs across regions of the human cortical hierarchy

The primate neocortex is organized as hierarchical networks of functionally distinct regions. In the dorsal visual stream network, information is conveyed from primary visual (V1) to posterior parietal (PPC) and dorsolateral prefrontal (DLPFC) cortices. This information transfer is mediated primarily by layer 3 pyramidal neurons (L3PNs), which differ across these regions in morphology, excitability, and intracellular Ca2+ regulation. These region-specific L3PN properties may be influenced by alternative splicing (AS) of pre-mRNA, which occurs extensively in the human brain. To explore the potential impact of AS of region-specific L3PN properties, we analyzed RNA-seq data from pools of L3PNs dissected from human V1, PPC, and DLPFC. We found that <6% of genes with regional differences in expression also differed in AS. This finding indicates that the absence of transcriptional differences is insufficient to conclude that a gene does not contribute functional differences between regions. Additionally, there were numerous regional differences in AS, particularly between V1 and DLPFC or PPC L3PNs, which involved genes associated with neuron morphology and Ca2+ regulation; > 90% of these AS differences involved functionally relevant sequences (eg phosphorylation sites, etc.). These findings suggest AS contributes to region-specific L3PN properties relevant to the function of the dorsal visual stream.