Most DNA in the genomes of higher organisms does not code for proteins. RNA Polymerase II (Pol II) transcribes non-coding DNA into long non-coding RNAs (lncRNAs)， but biological roles of lncRNA are unclear. We find that mutations in the yeast lncRNA result in poor growth. Defective termination of transcription causes read-through transcription across the gene promoter. Read-through transcription localizes chromatin signatures associated with Pol II elongation to the promoter. The act of Pol II elongation across this promoter represses functional expression by a Transcriptional Interference (TI) mechanism. Atp16p function in the mitochondrial ATP-synthase complex promotes mitochondrial DNA stability. repression by TI through inefficient termination of therefore triggers mitochondrial genome loss. Our results expand the functional and mechanistic implications of non-coding DNA in eukaryotes by highlighting termination of nuclear lncRNA transcription as mechanism to stabilize an organellar genome.