An unusual form of transcriptional silencing in yeast ribosomal DNA.

Abstract

Generalized transcriptional repression of large chromosomal regions in Saccharomyces cerevisiae occurs at the silent mating loci and at telomeres and is mediated by the silent information regulator (SIR) genes. We have identified a novel form of transcriptional silencing in S. cerevisiae in the ribosomal DNA (rDNA) tandem array. Tyl retrotransposons marked with a weakened URA3 gene (Tyl-mURAS) efficiently integrated into rDNA. The tnURA3 marker in rDNA was transcriptionally silenced in a SIR2-dependent manner. METIS and LEU2 were also partially silenced, indicating that rDNA silencing may be quite general. Deletion of SIR4 enhanced mURA3 and METIS silencing, but deletion of SIRl or SIRS did not affect silencing, indicating that the mechanism of silencing differs from that at telomeres and silent mating loci. Deletion of SIR2 resulted in increased psoralen cross-linking of the rDNA in vivo, suggesting that a specific chromatin structure in rDNA down-regulates polymerase II promoters.

Distinct Roles for the Essential MYST Family HAT Esa1p in Transcriptional Silencing

“…Indeed, it had previously been observed that a Pol III reporter gene could be silenced in a SIR-dependent manner (Schnell and Rine, 1986). However, in contrast to early indications (Smith and Boeke, 1997), subsequent more sensitive analysis indicates that SIR2 does not affect rDNA transcription , but may instead affect firing of origins of rDNA replication (Pasero et al, 2002).…”

“…Many questions remain about the nature of the regulation of the transcriptional silencing of the remainder of the repeats (reviewed in Grummt and Pikaard, 2003). When it was discovered that Pol II-regulated genes that are engineered into the rDNA array are silenced in an epigenetic manner that is dependent on SIR2 (Bryk et al, 1997;Fritze et al, 1997;Smith and Boeke, 1997), the appealing possibility was raised that Pol I transcription itself might be at least partially regulated through heterochromatin-like SIR-dependent mechanisms. Indeed, it had previously been observed that a Pol III reporter gene could be silenced in a SIR-dependent manner (Schnell and Rine, 1986).…”

“…For example, Sir2p may affect origin firing within the rDNA and Esa1p may affect transcriptional regulation, yet both functions may be required for appropriate chromatin structure. Likewise, it is known that some regions of the rDNA array are more sen-sitive to SIR2-silencing than others (Smith and Boeke, 1997;Buck et al, 2002). It should prove interesting to map regional effects of ESA1 control by comparison.…”

“…Sir2p, an NAD-dependent histone deacetylase (Imai et al, 2000;Landry et al, 2000;Smith et al, 2000), is unique among the Sir proteins because it is important for silencing at all three loci (reviewed in Gottschling, 2000;Guarente, 2000;Shore, 2000;Moazed, 2001). Sir2p is part of the RENT complex and plays a role in rDNA silencing and rDNA chromatin structure that is mediated through its deacetylase activity (Bryk et al, 1997;Fritze et al, 1997;Smith and Boeke, 1997;Shou et al, 1999;Straight et al, 1999;Ghidelli et al, 2001). Sir2p also plays an important role in suppressing homologous recombination within the repetitive rDNA array, highlighting its contribution to chromatin structure at this locus (Gottlieb and Esposito, 1989).…”

Chronological and replicative life-span extension in Saccharomyces cerevisiae by increased dosage of alcohol dehydrogenase 1

“…To determine the age-dependent mortality, cell viability at different days of growth was compared by spreading serial dilutions (1 : 10) of the cultures on solid YPD plates followed by incubation at 30 uC for 3 days. Replicative life-span determinations were performed by micromanipulation, as described elsewhere (Smith & Boeke, 1997;Sinclair & Guarente, 1997), using a Singer MSM system 300 micromanipulator. Life-span analyses wer carried out on YPD plates twice independently with 60 cells per strain per experiment.…”