1. Multiplexed single-cell characterization of alternative polyadenylation regulators.
- Author
-
Kowalski MH, Wessels HH, Linder J, Dalgarno C, Mascio I, Choudhary S, Hartman A, Hao Y, Kundaje A, and Satija R
- Subjects
- Humans, Animals, Mice, Introns genetics, Transcriptome genetics, RNA, Messenger metabolism, RNA, Messenger genetics, Gene Expression Regulation, Polyadenylation, Single-Cell Analysis methods, Poly A metabolism
- Abstract
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., Competing Interests: Declaration of interests In the past 3 years, R.S. has received compensation from Bristol-Myers Squibb, ImmunAI, Resolve Biosciences, Nanostring, 10x Genomics, Neptune Bio, and the NYC Pandemic Response Lab. R.S., H.-H.W., and Y.H. are cofounders and equity holders of Neptune Bio. A.K. is a scientific cofounder of Ravel Biotechnology; is on the scientific advisory board of PatchBio, SerImmune, AINovo, TensorBio, and OpenTargets; is a consultant with Illumina; and owns shares in DeepGenomics, Immunai, and Freenome. J.L. is an employee of Calico Life Sciences, LLC, as of 11/21/2022. H.-H.W. and Y.H. are employees of Neptune Bio as of 8/1/2023., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF