Quantification of alternative 3′UTR isoforms from single cell RNA-seq data with scUTRquant

Although half of human genes use alternative polyadenylation (APA) to generate mRNA isoforms that encode the same protein but differ in their 3′UTRs, most single cell RNA-sequencing (scRNA-seq) pipelines only measure gene expression. Here, we describe an open-access pipeline, called scUTRquant (https://github.com/Mayrlab/scUTRquant), that measures gene and 3′UTR isoform expression from scRNA-seq data obtained from known cell types in any species. scUTRquant-derived gene and 3′UTR transcript counts were validated against standard methods which demonstrated their accuracy. 3′UTR isoform quantification was substantially more reproducible than previous methods. scUTRquant provides an atlas of high-confidence 3′ end cleavage sites at single-nucleotide resolution to allow APA comparison across mouse datasets. Analysis of 120 mouse cell types revealed that during differentiation genes either change their expression or they change their 3′UTR isoform usage. Therefore, we identified thousands of genes with 3′UTR isoform changes that have previously not been implicated in specific biological processes.