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CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators
Most mammalian genes have multiple polyA sites, representing a substantial source of transcript diversity that is governed by the cleavage and polyadenylation (CPA) regulatory machinery. To better understand how these proteins govern polyA site choice we introduce CPA-Perturb-seq, a multiplexed pert...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934614/ https://www.ncbi.nlm.nih.gov/pubmed/36798324 http://dx.doi.org/10.1101/2023.02.09.527751 |
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author | Kowalski, Madeline H. Wessels, Hans-Hermann Linder, Johannes Choudhary, Saket Hartman, Austin Hao, Yuhan Mascio, Isabella Dalgarno, Carol Kundaje, Anshul Satija, Rahul |
author_facet | Kowalski, Madeline H. Wessels, Hans-Hermann Linder, Johannes Choudhary, Saket Hartman, Austin Hao, Yuhan Mascio, Isabella Dalgarno, Carol Kundaje, Anshul Satija, Rahul |
author_sort | Kowalski, Madeline H. |
collection | PubMed |
description | Most mammalian genes have multiple polyA sites, representing a substantial source of transcript diversity that is governed by the cleavage and polyadenylation (CPA) regulatory machinery. To better understand how these proteins govern polyA site choice we introduce CPA-Perturb-seq, a multiplexed perturbation screen dataset of 42 known CPA regulators with a 3’ scRNA-seq readout that enables transcriptome-wide inference of polyA site usage. We develop a statistical framework to specifically identify perturbation-dependent changes in intronic and tandem polyadenylation, and discover modules of co-regulated polyA sites exhibiting distinct functional properties. By training a multi-task deep neural network (APARENT-Perturb) on our dataset, we delineate a cis-regulatory code that predicts responsiveness to perturbation and reveals interactions between distinct regulatory complexes. Finally, we leverage our framework to re-analyze published scRNA-seq datasets, identifying new regulators that affect the relative abundance of alternatively polyadenylated transcripts, and characterizing extensive cellular heterogeneity in 3’ UTR length amongst antibody-producing cells. Our work highlights the potential for multiplexed single-cell perturbation screens to further our understanding of post-transcriptional regulation in vitro and in vivo. |
format | Online Article Text |
id | pubmed-9934614 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-99346142023-02-17 CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators Kowalski, Madeline H. Wessels, Hans-Hermann Linder, Johannes Choudhary, Saket Hartman, Austin Hao, Yuhan Mascio, Isabella Dalgarno, Carol Kundaje, Anshul Satija, Rahul bioRxiv Article Most mammalian genes have multiple polyA sites, representing a substantial source of transcript diversity that is governed by the cleavage and polyadenylation (CPA) regulatory machinery. To better understand how these proteins govern polyA site choice we introduce CPA-Perturb-seq, a multiplexed perturbation screen dataset of 42 known CPA regulators with a 3’ scRNA-seq readout that enables transcriptome-wide inference of polyA site usage. We develop a statistical framework to specifically identify perturbation-dependent changes in intronic and tandem polyadenylation, and discover modules of co-regulated polyA sites exhibiting distinct functional properties. By training a multi-task deep neural network (APARENT-Perturb) on our dataset, we delineate a cis-regulatory code that predicts responsiveness to perturbation and reveals interactions between distinct regulatory complexes. Finally, we leverage our framework to re-analyze published scRNA-seq datasets, identifying new regulators that affect the relative abundance of alternatively polyadenylated transcripts, and characterizing extensive cellular heterogeneity in 3’ UTR length amongst antibody-producing cells. Our work highlights the potential for multiplexed single-cell perturbation screens to further our understanding of post-transcriptional regulation in vitro and in vivo. Cold Spring Harbor Laboratory 2023-02-10 /pmc/articles/PMC9934614/ /pubmed/36798324 http://dx.doi.org/10.1101/2023.02.09.527751 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator. |
spellingShingle | Article Kowalski, Madeline H. Wessels, Hans-Hermann Linder, Johannes Choudhary, Saket Hartman, Austin Hao, Yuhan Mascio, Isabella Dalgarno, Carol Kundaje, Anshul Satija, Rahul CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators |
title | CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators |
title_full | CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators |
title_fullStr | CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators |
title_full_unstemmed | CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators |
title_short | CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators |
title_sort | cpa-perturb-seq: multiplexed single-cell characterization of alternative polyadenylation regulators |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934614/ https://www.ncbi.nlm.nih.gov/pubmed/36798324 http://dx.doi.org/10.1101/2023.02.09.527751 |
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