RNA polymerase switch in transcription of yeast rDNA: Role of transcription factor UAF (upstream activation factor) in silencing rDNA transcription by RNA polymerase II

Vu, Loan; Siddiqi, Imran; Lee, Bum-Soo; Josaitis, Cathleen A.; Nomura, Masayasu

doi:10.1073/pnas.96.8.4390

Cited by 61 publications

(103 citation statements)

References 39 publications

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“…Although its expression was shown to be responsive to Sir2, we did not observe high levels of K4-trimethylated H3 over the TAR1 ORF. Previous studies have characterized mutants that lack subunits of Pol I and survive by transcribing the 35S rRNA genes with Pol II (Conrad-Webb and Butow, 1995;Vu et al, 1999). However, in RNA from sir2⌬ cells, Pol II-derived 35S rRNA transcripts have not been detected (Oakes et al, 1999(Oakes et al, , 2006.…”

Section: Other Pol II Transcription Units In the Rdnamentioning

confidence: 99%

Sir2 Represses Endogenous Polymerase II Transcription Units in the Ribosomal DNA Nontranscribed Spacer

Mueller

Bryk

2006

MBoC

101

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Silencing at the rDNA, HM loci, and telomeres in Saccharomyces cerevisiae requires histone-modifying enzymes to create chromatin domains that are refractory to recombination and RNA polymerase II transcription machineries. To explore how the silencing factor Sir2 regulates the composition and function of chromatin at the rDNA, the association of histones and RNA polymerase II with the rDNA was measured by chromatin immunoprecipitation. We found that Sir2 regulates not only the levels of K4-methylated histone H3 at the rDNA but also the levels of total histone H3 and RNA polymerase II. Furthermore, our results demonstrate that the ability of Sir2 to limit methylated histones at the rDNA requires its deacetylase activity. In sir2⌬ cells, high levels of K4-trimethylated H3 at the rDNA nontranscribed spacer are associated with the expression of transcription units in the nontranscribed spacer by RNA polymerase II and with previously undetected alterations in chromatin structure. Together, these data suggest a model where the deacetylase activity of Sir2 prevents euchromatinization of the rDNA and silences naturally occurring intergenic transcription units whose expression has been associated with disruption of cohesion complexes and repeat amplification at the rDNA. INTRODUCTIONModified histones at silent genomic domains contribute to a chromatin environment that is refractory to gene expression and genetic recombination (reviewed in Strahl and Allis, 2000;Turner, 2000;Jenuwein and Allis, 2001). In Saccharomyces cerevisiae, chromatin at the homothallic mating-type loci HML and HMR, telomeres, and the ribosomal DNA locus (rDNA) silences genetic recombination and expression of native and ectopic genes transcribed by RNA polymerase (Pol) II. Silencing at the HM loci and telomeres has been studied extensively, whereas the mechanisms of Pol II silencing at the rDNA are not well characterized (reviewed in Moazed, 2001;Rusche et al., 2003). Increasing our understanding of the factors and mechanisms that regulate silencing at the rDNA will provide insight into the pathways that regulate gene expression and genome stability.In S. cerevisiae, the rDNA contains ϳ150 -200 tandem copies of a 9.1-kilobase (kb) repeat, with each repeat containing a Pol I-transcribed 35S rRNA gene and a nontranscribed spacer (NTS) that is subdivided into NTS1 and NTS2 by the Pol III-transcribed 5S rRNA gene (reviewed in Warner, 1999; Figure 1). Despite high levels of transcription by Pol I and Pol III in the rDNA locus, Pol II-transcribed genes integrated into the rDNA are silenced (referred to as rDNA silencing) (Bryk et al., 1997;Fritze et al., 1997;Smith and Boeke, 1997). Additionally, silent chromatin at the rDNA is essential for repression of genetic recombination (Gottlieb and Esposito, 1989;Davis et al., 2000;Kobayashi et al., 2004) and extension of replicative life span (reviewed in Guarente, 2000).Chromatin-associated proteins and modified histones regulate silencing of Pol II transcription at the rDNA (Bryk et al., 1997;Fritze et al., 199...

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Section: Other Pol II Transcription Units In the Rdnamentioning

confidence: 99%

Sir2 Represses Endogenous Polymerase II Transcription Units in the Ribosomal DNA Nontranscribed Spacer

Mueller

Bryk

2006

MBoC

101

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“…These strains grow well on galactose, using GAL7-35S rDNA helper plasmids for transcription of rRNA, but produce a low frequency of variants that can also grow on glucose, where transcription of the GAL7 promoter is repressed. We called these variants PSW, for polymerase switched, and we called the original galactose-dependent strain N-PSW, for no good growth, polymerase switched, and we demonstrated Pol II transcription (and no Pol I transcription) of chromosomal rDNA in both of these strains (17,20). As with rrn9⌬, disruptions in genes for the UAF components RRN5 and RRN10 give similar results.…”

Section: Resultsmentioning

confidence: 58%

“…We originally discovered the polymerase switching phenomenon in strains carrying deletions in the UAF component RRN9 (20). These strains grow well on galactose, using GAL7-35S rDNA helper plasmids for transcription of rRNA, but produce a low frequency of variants that can also grow on glucose, where transcription of the GAL7 promoter is repressed.…”

Section: Resultsmentioning

confidence: 99%

“…Total RNA was prepared and primer extension analysis was carried out using a ␥-32 P-labeled primer which hybridizes to the 35S rRNA external transcribed spacer, as described previously (20). Autoradiograms were quantitated by a PhosphorImager.…”

Section: Methodsmentioning

confidence: 99%

“…Thus, they concluded that high levels of TBP can bypass the requirement for UAF and that TBP directly stimulates transcription from the core transcriptional machinery (1). We found previously that mutations in UAF components immediately lead to a polymerase switch in rRNA transcription from Pol I to Pol II (17,20). This state is called N-PSW.…”

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confidence: 93%

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Role of TATA Binding Protein (TBP) in Yeast Ribosomal DNA Transcription by RNA Polymerase I: Defects in the Dual Functions of Transcription Factor UAF Cannot Be Suppressed by TBP

Siddiqi

Keener

et al. 2001

Molecular and Cellular Biology

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. Here, we demonstrate that deletions in the UAF component RRN5, RRN9, or RRN10 lead to Pol II transcription of rDNA. TBP overexpression does not suppress UAF mutation, and these strains continue to use Pol II for rRNA transcription. We do not find evidence for even low levels of Pol I transcription in UAF mutant strains carrying overexpressed TBP. In diploid strains lacking both copies of the UAF component RRN9, Pol II transcription of rDNA is more strongly repressed than in haploid strains but TBP overexpression still fails to activate Pol I. These results emphasize that UAF plays an essential role in activation of Pol I transcription and silencing of Pol II transcription of rDNA and that TBP functions to recruit the Pol I machinery in a manner completely dependent on UAF.

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Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription?

Yague‐Sanz

2023

Yeast

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Eukaryotic genes must be condensed into chromatin while remaining accessible to the transcriptional machinery to support gene expression. Among the three eukaryotic RNA polymerases (RNAP), RNAPII is unique, partly because of the C‐terminal domain (CTD) of its largest subunit, Rpb1. Rpb1 CTD can be extensively modified during the transcription cycle, allowing for the co‐transcriptional recruitment of specific interacting proteins. These include chromatin remodeling factors that control the opening or closing of chromatin. How the CTD‐less RNAPI and RNAPIII deal with chromatin at rRNA and tRNA genes is less understood. Here, we review recent advances in our understanding of how the chromatin at tRNA genes and rRNA genes can be remodeled in response to environmental cues in yeast, with a particular focus on the role of local RNAPII transcription in recruiting chromatin remodelers at these loci. In fission yeast, RNAPII transcription at tRNA genes is important to re‐establish a chromatin environment permissive to tRNA transcription, which supports growth from stationary phase. In contrast, local RNAPII transcription at rRNA genes correlates with the closing of the chromatin in starvation in budding and fission yeast, suggesting a role in establishing silent chromatin. These opposite roles might support a general model where RNAPII transcription recruits chromatin remodelers to tRNA and rRNA genes to promote the closing and reopening of chromatin in response to the environment.

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RNA polymerase switch in transcription of yeast rDNA: Role of transcription factor UAF (upstream activation factor) in silencing rDNA transcription by RNA polymerase II

Cited by 61 publications

References 39 publications

Sir2 Represses Endogenous Polymerase II Transcription Units in the Ribosomal DNA Nontranscribed Spacer

Sir2 Represses Endogenous Polymerase II Transcription Units in the Ribosomal DNA Nontranscribed Spacer

Role of TATA Binding Protein (TBP) in Yeast Ribosomal DNA Transcription by RNA Polymerase I: Defects in the Dual Functions of Transcription Factor UAF Cannot Be Suppressed by TBP

Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription?

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