Single-cell landscape and regulation of alternative polyadenylation in the brain

As so far, the trans-regulation of alternative polydenylation (APA) are poorly understood. In this study, we de novo predicted multiple APA regulators based on large-scale single-cell data and detected some potential regulators, including PABPN1, SF3B4, U2AF2, HDAC1 and PCBP2. To further validate the function of these potential regulators, we generated two biological replicates of knock-down lines for each gene in HEK293T, and then carried out RNA-seq experiments after extracting nuclei to measure the transcriptome-wide APA usage difference. APA profiling analysis of RNA-seq data from HEK293T cells after knocking down APA regulators, including PABPN1, SF3B4, U2AF2, HDAC1 and PCBP2.