%0 Journal Article
%T Multiplexed single-cell characterization of alternative polyadenylation regulators.
%A Kowalski MH
%A Wessels HH
%A Linder J
%A Dalgarno C
%A Mascio I
%A Choudhary S
%A Hartman A
%A Hao Y
%A Kundaje A
%A Satija R
%J Cell
%V 187
%N 16
%D 2024 Aug 8
%M 38925112
%F 66.85
%R 10.1016/j.cell.2024.06.005
%X Most mammalian genes have multiple polyA sites, representing a substantial source of transcript diversity regulated by the cleavage and polyadenylation (CPA) machinery. To better understand how these proteins govern polyA site choice, we introduce CPA-Perturb-seq, a multiplexed perturbation screen dataset of 42 CPA regulators with a 3' scRNA-seq readout that enables transcriptome-wide inference of polyA site usage. We develop a framework to detect perturbation-dependent changes in polyadenylation and characterize modules of co-regulated polyA sites. We find groups of intronic polyA sites regulated by distinct components of the nuclear RNA life cycle, including elongation, splicing, termination, and surveillance. We train and validate a deep neural network (APARENT-Perturb) for tandem polyA site usage, delineating a cis-regulatory code that predicts perturbation response and reveals interactions between regulatory complexes. Our work highlights the potential for multiplexed single-cell perturbation screens to further our understanding of post-transcriptional regulation.