UC Berkeley

Transcription of RNA antisense to protein-coding genes is widespread in genomes from bacteria to human. For most antisense transcription, the methods by which it is regulated and its potential function remain unknown. We sought to address these questions, using budding yeast as a model system, with two complementary approaches. First, we mapped antisense expression in four Saccharomyces species. Antisense transcripts conserved across yeasts were predominantly detected at open reading frames in a tail-to-head orientation with respect to the next gene 3' to the reference gene. For such tandem gene pairs, the region between the genes exhibited distinctive signatures of binding by transcription factors, suggesting that these factors could regulate transcription of both the mRNA from the 3' gene and the upstream antisense transcript. Transcription factor deletion experiments supported this hypothesis, conferring decreased expression of both antisense and downstream sense transcripts at such gene pairs; often in these mutants, as an antisense transcript dropped in expression, its host gene mRNA level increased, a hallmark of antisense-mediated repression. To test this model, we focused on the stress-response gene YKL151C and its downstream neighbor GPM1, which was strongly expressed in rich media. Cis-regulatory mutation experiments showed that YKL151C antisense expression was co-regulated with GPM1 and repressed mRNA levels of its overlapping sense transcript. In a second body of work, we used natural variation rather than engineered mutations to access the impact of variants that modulate antisense expression levels. We mapped naturally occurring polymorphisms between yeast strains that showed linkage to sense and antisense expression. We identified cases where such regulatory polymorphisms mediated their effects through transcription factors that bound at the promoters of linked antisense transcripts; in all such cases, expression of the downstream gene also showed linkage to the polymorphism, and, in several cases, sense transcription overlapping the antisense was linked as well. Our studies thus converged on a model in which antisense transcription at one yeast gene frequently originates from and is co-regulated with the promoter of a neighboring gene, mediated by the action of transcription factors; at a fraction of such loci, antisense transcription acts to repress expression of its overlapping mRNA, enabling the joint control of adjacent genes specialized to opposing conditions.