biostudies-literatureKang BNIMH NIH HHSNational Institute of Mental HealthNational Institute of General Medical SciencesNIGMS NIH HHSNational Science Foundation1774-1787https://www.ebi.ac.uk/biostudies/studies/S-EPMC10691540biostudies-literatureUnknown33(10)Differential polyadenylation sites (PAs) critically regulate gene expression, but their cell type-specific usage and spatial distribution in the brain have not been systematically characterized. Here, we present Infernape, which infers and quantifies PA usage from single-cell and spatial transcriptomic data and show its application in the mouse brain. Infernape uncovers alternative intronic PAs and 3'-UTR lengthening during cortical neurogenesis. Progenitor-neuron comparisons in the excitatory and inhibitory neuron lineages show overlapping PA changes in embryonic brains, suggesting that the neural proliferation-differentiation axis plays a prominent role. In the adult mouse brain, we uncover cell type-specific PAs and visualize such events using spatial transcriptomic data. Over two dozen neurodevelopmental disorder-associated genes such as <i>Csnk2a1</i> and <i>Mecp2</i> show differential PAs during brain development. This study presents Infernape to identify PAs from scRNA-seq and spatial data, and highlights the role of alternative PAs in neuronal gene regulation.Genome researchInfernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.PMC10691540DMS-2238656T32 GM139782DP2 GM137423R01 MH130594DMS-2113646Lee PYang YRuan XKang BLiu YLZhang XLee JHu KWang JfalseInfernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.Differential polyadenylation sites (PAs) critically regulate gene expression, but their cell type-specific usage and spatial distribution in the brain have not been systematically characterized. Here, we present Infernape, which infers and quantifies PA usage from single-cell and spatial transcriptomic data and show its application in the mouse brain. Infernape uncovers alternative intronic PAs and 3'-UTR lengthening during cortical neurogenesis. Progenitor-neuron comparisons in the excitatory and inhibitory neuron lineages show overlapping PA changes in embryonic brains, suggesting that the neural proliferation-differentiation axis plays a prominent role. In the adult mouse brain, we uncover cell type-specific PAs and visualize such events using spatial transcriptomic data. Over two dozen neurodevelopmental disorder-associated genes such as <i>Csnk2a1</i> and <i>Mecp2</i> show differential PAs during brain development. This study presents Infernape to identify PAs from scRNA-seq and spatial data, and highlights the role of alternative PAs in neuronal gene regulation.2023-01-01T00:00:00Z2023 Oct2026-06-12T05:27:58.227Z2025-04-04T09:39:39.958ZS-EPMC106915403790732810.1101/gr.277864.123