ArticleGenome research2023
Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A flexible and unified framework for single- and multi-outcome Mendelian randomization using summary statistics.American journal of human genetics · 2026Article
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- 3'UTR shortening alleviates miRNA repression of mRNAs critical for muscle stem cell differentiation.The EMBO journal · 2026Article
- metaAPA: a tool for integration of PolyA site predictions from single-cell and spatial transcriptomics.Bioinformatics advances · 2026Article
- Multitissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs.Genome research · 2025Article
- scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data.Genome biology · 2025Article
- Quantification of transcript isoforms at the single-cell level using SCALPEL.Nature communications · 2025Article
- Review
- Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders.Research square · 2024Article
- Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders.Npj biological timing and sleep · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
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
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