Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

摘要

Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation ofgene expression across eukaryotes. Although APA is extensively studied, its regulationwithin cellular compartments and its physiological impact remains largely enigmatic. Here,we employed a rigorous subcellular fractionation approach to compare APA profiles ofcytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us toextract APA isoforms that are subjected to differential regulation and provided us with aplatform to interrogate the molecular regulatory pathways that shape APA profiles indifferent subcellular locations. Here we show that APA isoforms with shorter 3’UTRs tendto be overrepresented in the cytoplasm and appear to be cell type specific events. Nuclearretention of longer APA isoforms occurs and is partly a result of incomplete splicingcontributing to the observed cytoplasmic bias of transcripts with shorter 3’UTRs. Wedemonstrate that the endoribonuclease III, DICER1, contributes to the establishment ofsubcellular APA profiles not only by expected cytoplasmic miRNA mediated destabilisationof APA mRNA isoforms, but also by affecting polyadenylation site choice.