Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation Jonathan Neve1#, Kaspar Burger2#, Wencheng Li3, Mainul Hoque3, Radhika Patel1, Bin Tian3, Monika Gullerova2* and Andre Furger1* Affiliations: 1 Department of Biochemistry, South Parks Road, University of Oxford, OX1 3QU, UK 2 Sir William Dunn School of Pathology, South Parks Road, University of Oxford, OX1 3RE, UK 3Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA *Corresponding authors: Andre Furger Email:
[email protected] Monika Gullerova Email:
[email protected] # authors contributed equally Running Title: APA and subcellular fractionation Key words: alternative polyadenylation, mRNA, subcellular fractionation, DICER1 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press 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 employed 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.