Alternative 3' Polyadenylation Responses to Acute Ethanol Exposure Differ Between Drosophila Populations

Alternative polyadenylation is a pervasive post-transcriptional mechanism that generates mRNA isoforms with distinct 3' untranslated regions (3' UTRs), which can influence transcript stability, localization and translation. Ethanol is an environmental stressor for Drosophila melanogaster, and natural populations show distinct responses to ethanol exposure, suggesting that the genetic background can modulate phenotypic response. Yet, how the natural genetic variation modulates ethanol-responsive APA remains understudied. We profiled 3' end isoforms following acute ethanol exposure in three French (cosmopolitan) and three Zambian (ancestral range) D. melanogaster genotypes and identified numerous significant APA events across all genotypes. Ethanol-induced APA was widespread but highly genotype - and population - dependent: the French genotypes showed an enrichment of proximal shifts (3' UTR shortening), while Zambian genotypes were biased toward distal shifts (3' UTR lengthening). Most of the ethanol-responsive APA events were private to a single population, with relatively few genes exhibiting conserved directional changes across both backgrounds. We also classify genes showing opposite-direction shifts between populations, and others with opposite-direction shifts between various classes of APA. For two-site events, inter-poly(A) site distance did not predict response direction; however, spacing strongly predicted the magnitude of remodeling, with larger separations enabling greater absolute 3' UTR length changes. Our findings support a model in which ethanol-responsive 3' end regulation is a flexible genetically contingent, and that population-specific APA remodeling represent a plausible molecular substrate contributing to adaptation.