The landscape of alternative polyadenylation in single cells of the developing mouse embryo

39 untranslated regions (39 UTRs) post-transcriptionally regulate mRNA stability, localization, and translation rate. While 39-UTR isoforms have been globally quantified in limited cell types using bulk measurements, their differential usage among cell types during mammalian development remains poorly characterized. In this study, we examined a dataset comprising ~2 million cells spanning E9.5-E13.5 of mouse embryonic development to quantify transcriptome-wide changes in alternative polyadenylation (APA). We observe a global lengthening of 39 UTRs across embryonic stages in all cell types, although we detect shorter 39 UTRs in hematopoietic lineages and longer 39 UTRs in neuronal cell types within each stage. While the majority of individual genes possess 39 UTRs that lengthen with time, a subset appear to be spatiotemporally regulated through APA. By measuring 39-UTR isoforms in an expansive single cell dataset, our work provides a transcriptome-wide and organism-wide map of the dynamic landscape of alternative polyadenylation during mammalian organogenesis.