{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kang B"],"funding":["NIMH NIH HHS","National Institute of Mental Health","National Institute of General Medical Sciences","NIGMS NIH HHS","National Science Foundation"],"pagination":["1774-1787"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10691540"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["33(10)"],"pubmed_abstract":["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."],"journal":["Genome research"],"pubmed_title":["Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain."],"pmcid":["PMC10691540"],"funding_grant_id":["DMS-2238656","T32 GM139782","DP2 GM137423","R01 MH130594","DMS-2113646"],"pubmed_authors":["Lee P","Yang Y","Ruan X","Kang B","Liu YL","Zhang X","Lee J","Hu K","Wang J"],"additional_accession":[]},"is_claimable":false,"name":"Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.","description":"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.","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Oct","modification":"2026-06-12T05:27:58.227Z","creation":"2025-04-04T09:39:39.958Z"},"accession":"S-EPMC10691540","cross_references":{"pubmed":["37907328"],"doi":["10.1101/gr.277864.123"]}}