A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA

Coelho, P. S. R.; Bryan, Anthony C.; Kumar, Anuj; Shadel, Gerald S.; Snyder, M

doi:10.1101/gad.1035002

Cited by 70 publications

(79 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A naturally occurring Pol II-transcribed gene TAR1 has been identified on the antisense strand of the 35S rRNA gene ϳ3-4 kb away from NTS2 (Coelho et al, 2002). Although its expression was shown to be responsive to Sir2, we did not observe high levels of K4-trimethylated H3 over the TAR1 ORF.…”

Section: Other Pol II Transcription Units In the Rdnamentioning

confidence: 41%

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

Mueller

Bryk

2006

MBoC

101

View full text Add to dashboard Cite

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...

show abstract

Section: Other Pol II Transcription Units In the Rdnamentioning

confidence: 41%

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

Mueller

Bryk

2006

MBoC

101

View full text Add to dashboard Cite

show abstract

“…Moreover, although small ORFs are known to be encoded within ncRNA-coding genes (e.g., Tar1p in rRNA; ref. 29), the result reported here is a demonstration of the opposite phenomenon: small RNAs being encoded antisense to the protein-coding sequence.…”

Section: Resultsmentioning

confidence: 65%

Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway

Samanta

Tongprasit

Sethi

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Noncoding RNAs (ncRNAs) perform essential cellular tasks and play key regulatory roles in all organisms. Although several new ncRNAs in yeast were recently discovered by individual studies, to our knowledge no comprehensive empirical search has been conducted. We demonstrate a powerful and versatile method for global identification of previously undescribed ncRNAs by modulating an essential RNA processing pathway through the depletion of a key ribonucleoprotein enzyme component, and monitoring differential transcriptional activities with genome tiling arrays during the time course of the ribonucleoprotein depletion. The entire Saccharomyces cerevisiae genome was scanned during cell growth decay regulated by promoter-mediated depletion of Rpp1, an essential and functionally conserved protein component of the RNase P enzyme. In addition to most verified genes and ncRNAs, expression was detected in 98 antisense and intergenic regions, 74 that were further confirmed to contain previously undescribed RNAs. A class of ncRNAs, located antisense to coding regions of verified protein-coding genes, is discussed in this article. One member, HRA1, is likely involved in 18S rRNA maturation.HRA1 ͉ microarray ͉ RNase P ͉ yeast

show abstract

“…While initially characterized using reporter genes, rDNA silencing was eventually found to regulate TAR1, a mitochondrial protein gene encoded on the antisense strand of the 35S transcribed region (Coelho et al 2002). RENT also represses noncoding RNAs expressed from NTS1 and NTS2 Vasiljeva et al 2008).…”

Section: Sir2-mediated Rdna Stabilization and Silencingmentioning

confidence: 99%

The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae

2016

View full text Add to dashboard Cite

Transcriptional silencing in Saccharomyces cerevisiae occurs at several genomic sites including the silent mating-type loci, telomeres, and the ribosomal DNA (rDNA) tandem array. Epigenetic silencing at each of these domains is characterized by the absence of nearly all histone modifications, including most prominently the lack of histone H4 lysine 16 acetylation. In all cases, silencing requires Sir2, a highly-conserved NAD + -dependent histone deacetylase. At locations other than the rDNA, silencing also requires additional Sir proteins, Sir1, Sir3, and Sir4 that together form a repressive heterochromatin-like structure termed silent chromatin. The mechanisms of silent chromatin establishment, maintenance, and inheritance have been investigated extensively over the last 25 years, and these studies have revealed numerous paradigms for transcriptional repression, chromatin organization, and epigenetic gene regulation. Studies of Sir2-dependent silencing at the rDNA have also contributed to understanding the mechanisms for maintaining the stability of repetitive DNA and regulating replicative cell aging. The goal of this comprehensive review is to distill a wide array of biochemical, molecular genetic, cell biological, and genomics studies down to the "nuts and bolts" of silent chromatin and the processes that yield transcriptional silencing.

show abstract

A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA

Cited by 70 publications

References 26 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

Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway

The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae

Contact Info

Product

Resources

About