title: Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation.
abstract: Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here, we show that APA isoforms with shorter 3' UTRs tend to be overrepresented in the cytoplasm and appear to be cell-type-specific events. Nuclear retention of longer APA isoforms occurs and is partly a result of incomplete splicing contributing to the observed cytoplasmic bias of transcripts with shorter 3' UTRs. We demonstrate that the endoribonuclease III, DICER1, contributes to the establishment of subcellular APA profiles not only by expected cytoplasmic miRNA-mediated destabilization of APA mRNA isoforms, but also by affecting polyadenylation site choice.
authors.affiliation: Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom;
authors.forename: Jonathan
authors.initials: J
authors.lastname: Neve
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom;
authors.forename: Kaspar
authors.initials: K
authors.lastname: Burger
authors.affiliation: Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA.
authors.forename: Wencheng
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA.
authors.forename: Mainul
authors.initials: M
authors.lastname: Hoque
authors.affiliation: Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom;
authors.forename: Radhika
authors.initials: R
authors.lastname: Patel
authors.affiliation: Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Tian
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom;
authors.forename: Monika
authors.initials: M
authors.lastname: Gullerova
authors.affiliation: Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom;
authors.forename: Andre
authors.initials: A
authors.lastname: Furger
mesh_terms: D020413:3' Untranslated Regions; D053487:DEAD-box RNA Helicases / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056511:Metallochaperones / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D026723:Polyadenylation; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing; D020871:RNA Stability; D043244:Ribonuclease III / Q000235:genetics* / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; C112111:CIAO1 protein, human; D056511:Metallochaperones; D035683:MicroRNAs; D020033:Protein Isoforms; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases