The tripartite Rpd3/Sin3/Ume6 complex represses meiotic isoforms during mitosis. We asked if it also controls starvation-induced isoforms. We report thatVTH1/VTH2encode acetate-inducible isoforms with extended 5′-regions overlapping antisense long non-coding RNAs. Rpd3 and Ume6 repress the long isoform ofVTH2during fermentation. Cells metabolising glucose contain Vth2, while the protein is undetectable in acetate and during sporulation.VTH2is a useful model locus to study mechanisms implicating promoter directionality, lncRNA transcription and post-transcriptional control of gene expression via 5′-UTRs. Since mammalian genes encode transcript isoforms and Rpd3 is conserved, our findings are relevant for gene expression in higher eukaryotes.