Abstract: In S. cerevisiae the repeated units of the ribosomal locus, transcribed by RNA polymerase I, are interrupted by non transcribed spacers. These NTS regions are transcribed by RNA polymerase III to synthesize 5S RNA and, by RNA Polymerase II to synthesize, at low level, non coding RNAs. While both RNA polymerase I and III transcriptions are highly characterized, at rDNA only few studies have been performed on Pol II, whose repression correlates with the SIR2-dependent silencing. The involvement of both chromatin organization and Pol I transcription has been proposed, and peculiar chromatin structures might justify "ribosomal" Pol II silencing. Reporter genes, inserted within the rDNA units, have been employed for these studies. We studied, in the natural context, yeast mutants differing in Pol I transcription in order to find whether correlations exist between Pol I transcription and Pol II ncRNAs production. Here, we demonstrate that silencing at rDNA represses ncRNAs with a strength inversely proportional to Pol I transcription. Moreover, localized regions of histone hyperacetylation appear, in cryptic promoter elements, when Pol II is active and in the coding region when Pol I is functional; in addition, DNA topoisomerase I site-specific activity follows RNA polymerase I transcription. The repression of ncRNAs at rDNA, in response to RNA polymerase I transcription, could represent a physiological circuit control whose mechanism involves modification of histone acetylation.