Transcriptional activity and chromatin structure of enhancer-deleted rRNA genes in Saccharomyces cerevisiae

We used the psoralen gel retardation assay and Northern blot analysis in an in vivo yeast system to analyze effects of rDNA enhancer deletions on the chromatin structure and the transcription of tagged rDNA units. We found th at upon deletion of a single enhancer element, transcription of the upstrea m and downstream rRNA gene was reduced by about 50%. Although removing both banking enhancers of an rRNA gene led to a further reduction in transcript ion levels, a significant amount of transcriptional activity remained, eith er resulting from the influence of more distantly located enhancer elements or reflecting the basal activity of the polymerase I promoter within the n ucleolus. Despite the reduction of transcriptional activity upon enhancer d eletion, the activation frequency (proportion of nonnucleosomal to nucleoso mal gene copies in a given cell culture) of the tagged rRNA genes was not s ignificantly altered, as determined by the psoralen gel retardation assay. This is a strong indication that, within the nucleolus, the yeast rDNA enha ncer functions by increasing transcription rates of active rRNA genes and n ot by activating silent transcription units.