Expression of yeast 5S RNA is independent of the rDNA enhancer region

In the yeast Saccharomyces cerevisiae, each of the tandemly repeated ribosomal RNA genes carries a 5S gene within the 'non-transcribed' spacer region. These 5S RNA genes lie between the rDNA enhancer and the promoter of rRNA transcription. Since there is roughly equimolar synthesis of 5S RNA and the 35S rRNA precursor transcript we asked whether the enhancer plays a role in regulating the transcription of 5S RNA. A marked 5S gene was inserted into plasmids designed to test rDNA enhancer function. The enhancer failed to stimulate 5S RNA synthesis even though it stimulated transcription of a distal rRNA test gene greater than 10-fold. This failure is consistent with a model of enhancer function that proposes specific interactions between the enhancer and the 35S rRNA promoter via a looping out of the intervening 5S RNA gene.