RNA Polymerase I Transcription Silences Noncoding RNAs at the Ribosomal DNA Locus in Saccharomyces cerevisiae

Abstract

In Saccharomyces cerevisiae the repeated units of the ribosomal locus, transcribed by RNA polymerase I (Pol I), are interrupted by nontranscribed spacers (NTSs). These NTS regions are transcribed by RNA polymerase III to synthesize 5S RNA and by RNA polymerase II (Pol II) to synthesize, at low levels, noncoding RNAs (ncRNAs). While transcription of both RNA polymerase I and III is highly characterized, at the ribosomal DNA (rDNA) locus only a 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 ncRNA production. Here, we demonstrate that silencing at the rDNA locus 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 the rDNA locus, in response to RNA polymerase I transcription, could represent a physiological circuit control whose mechanism involves modification of histone acetylation.

The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae

“…Supporting this idea, rDNA silencing of Pol II transcription actually requires Pol I transcription. Mutants lacking Pol I activity are defective for rDNA silencing, regardless of whether the reporter or endogenous noncoding genes are located in NTS1, NTS2, or 35S regions (Buck et al 2002;Cioci et al 2003;Cesarini et al 2010). Therefore, transcription of the rDNA genes by Pol I also has a much broader and undefined role in rDNA silencing outside its function in recruiting RENT.…”

“…rDNA stability and the silencing of Pol II transcription in the rDNA While rDNA silencing was initially discovered fortuitously with reporter genes, study of the phenomenon ultimately led to the realization that Pol II naturally transcribes the NTS1 and NTS2 elements that are repressed by Sir2 ( Figure 12C) Li et al 2006;Vasiljeva et al 2008;Cesarini et al 2010). Such noncoding RNAs are derived from NTS1 and NTS2, and range in size from 1000 to 1700 nt.…”

The Epigenetic Pathways to Ribosomal DNA Silencing

“…RNAPII transcription of rDNA starts from two promoters, called cryptic RNAPII promoter (C-Pro) and EXP promoter (E-Pro). The intergenic cryptic transcripts are produced from C-Pro and E-Pro (200). (B and C) Human rDNA (43 kb) and mouse rDNA (45.3 kb) consist of 5.8S, 18S, and 28S transcribed genes; ITS1 and ITS2; and a long NTS called an IGS (intergenic spacer).…”

Alternative Chromatin Structures of the 35S rRNA Genes in Saccharomyces cerevisiae Provide a Molecular Basis for the Selective Recruitment of RNA Polymerases I and II

“…The fact that a single factor controls promoter usage by different RNA polymerases is so far a unique feature of UAF, but the mechanism remains ill defined. UAF is also important for silencing of Pol II reporter genes integrated into the rDNA locus (9) and the Pol II-dependent production of noncoding RNAs (ncRNAs) within IGS1 and IGS2 (7). Efficient silencing of Pol II transcription in rDNA further depends on Pol I transcription (7,9) and on the histone deacetylase Sir2 together with Net1 and Cdc14 forming the RENT complex (4,12,39,41).…”

“…UAF is also important for silencing of Pol II reporter genes integrated into the rDNA locus (9) and the Pol II-dependent production of noncoding RNAs (ncRNAs) within IGS1 and IGS2 (7). Efficient silencing of Pol II transcription in rDNA further depends on Pol I transcription (7,9) and on the histone deacetylase Sir2 together with Net1 and Cdc14 forming the RENT complex (4,12,39,41). This has led to the model that UAF, perhaps together with other Pol I-associated factors, nucleates a special chromatin structure at the Pol I promoter, being repressive for 35S rRNA synthesis by Pol II and spreading to other rDNA regions by factors like RENT (9).…”