Silencing in Yeast rDNA Chromatin

Cioci, Francesco; Vu, Loan; Eliason, Kristilyn; Oakes, Melanie L.; Siddiqi, Imran; Nomura, Masayasu

doi:10.1016/s1097-2765(03)00262-4

Cited by 75 publications

(33 citation statements)

References 40 publications

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“…This is supported by evidence that suggests a reciprocal relationship between RNAP I and II transcription in the rDNA (62, 63). Thus the presence of rDNA repeats on the nucleus/nucleolus interface may free them up to be transcribed by RNAP II and/or III.…”

Section: Transcription and Nucleolus Directed Organizationmentioning

confidence: 67%

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

O’Sullivan¹,

Pai²,

Cridge

et al. 2013

BioMolecular Concepts

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The nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribosomes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfil the cellular demand for rRNA, the ribosomal RNA genes (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our comprehension of genome and transcriptional organization in cells. In this review we address the question of whether the nucleolus is a raft adrift the sea of nuclear DNA, or actively contributes to genome organization. We present evidence supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis. We propose that the nucleolus and the rDNA are central factors in the spatial organization of the genome, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences. Finally, we discuss some predictions that result from the nucleolus having a central role in nuclear organization.

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Section: Transcription and Nucleolus Directed Organizationmentioning

confidence: 67%

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

O’Sullivan¹,

Pai²,

Cridge

et al. 2013

BioMolecular Concepts

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“…( E ) Effect of asf1 Δ in reduced rDNA repeat-number strains. ASF1 was deleted in previously described strains carrying approximately 190, approximately 25 or 2 rDNA repeats and lacking FOB1 (80,81), followed by four rounds of platings and PFGE analysis as in Figure 1B. Because growth of the 2-repeat strain is supported by GAL-driven rDNA expression from a plasmid with a TRP1 marker, all manipulations of this strain were performed on synthetic GAL plates lacking Tryptophan, and to maintain consistency in the experiment all manipulations of the approximately 190 and 25 repeat strains were performed on synthetic GAL plates.…”

Section: Resultsmentioning

confidence: 99%

Repeat expansion in the budding yeast ribosomal DNA can occur independently of the canonical homologous recombination machinery

Houseley¹,

Tollervey²

2011

Nucleic Acids Research

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Major eukaryotic genomic elements, including the ribosomal DNA (rDNA), are composed of repeated sequences with well-defined copy numbers that must be maintained by regulated recombination. Although mechanisms that instigate rDNA recombination have been identified, none are directional and they therefore cannot explain precise repeat number control. Here, we show that yeast lacking histone chaperone Asf1 undergo reproducible rDNA repeat expansions. These expansions do not require the replication fork blocking protein Fob1 and are therefore independent of known rDNA expansion mechanisms. We propose the existence of a regulated rDNA repeat gain pathway that becomes constitutively active in asf1Δ mutants. Cells lacking ASF1 accumulate rDNA repeats with high fidelity in a processive manner across multiple cell divisions. The mechanism of repeat gain is dependent on highly repetitive sequence but, surprisingly, is independent of the homologous recombination proteins Rad52, Rad51 and Rad59. The expansion mechanism is compromised by mutations that decrease the processivity of DNA replication, which leads to progressive loss of rDNA repeats. Our data suggest that a novel mode of break-induced replication occurs in repetitive DNA that is dependent on high homology but does not require the canonical homologous recombination machinery.

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“…Because the tRNA genes are nucleolar, it is particularly interesting that several gene deletions that affect Sir2p-dependent and Sir2p-independent rRNA gene cluster silencing (e.g. RPA34, RIF1, SET1, SIR2, SNF2) (12,13,22,23) do not affect tgm silencing. Although these results do not rule out involvement of some aspect of chromatin structure in tgm silencing, they suggest that its mechanism is fundamentally different from most other silencing forms.…”

Section: Resultsmentioning

confidence: 99%

Silencing Near tRNA Genes Requires Nucleolar Localization

Wang

Haeusler

Good

et al. 2005

Journal of Biological Chemistry

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Transcription by RNA polymerase II is antagonized by the presence of a nearby tRNA gene in Saccharomyces cerevisiae. To test hypotheses concerning the mechanism of this tRNA gene-mediated (tgm) silencing, the effects of specific gene deletions were determined. The results show that the mechanism of silencing near tRNA genes is fundamentally different from other forms of transcriptional silencing in yeast. Rather, tgm silencing is dependent on the ability to cluster the dispersed tRNA genes in or near the nucleolus, constituting a form of three-dimensional gene control.Chromatin-mediated transcriptional silencing has been extensively studied in Saccharomyces cerevisiae: at the two silent mating type loci, near telomeres, and in the single cluster of tandemly repeated rRNA genes (1). Mutations affecting these silencing forms affect chromatin structure by altering histone modifications and remodeling. Unlike other eukaryotes, S. cerevisiae appears to lack RNA-mediated forms of silencing (2).Actively transcribed tRNA genes can suppress transcription of nearby genes by RNA polymerase II (pol II) 1 in yeast (3,4). This phenomenon, termed either tRNA gene position effect (5) or tRNA gene-mediated (tgm) silencing (6), is independent of the tRNA gene orientation and does not involve simple steric blockage of RNA pol II upstream activator sites (6). It is dependent on transcription of the tRNA gene, since mutations in the pol III promoters and conditional mutations in RNA polymerase III (pol III) alleviate tgm silencing. The degree to which this effect suppresses nearby pol II transcription varies depending the pol II promoter (6).Unlike other silencing elements, tRNA genes are scattered throughout the genome in large numbers and could potentially influence neighboring genes, although pol II promoters are underrepresented near tRNA genes (5). Notable exceptions to this are the Ty retrotransposons (5,7,8), which appear to have adapted to the environment and preferentially insert near tRNA genes. The mechanism of tgm silencing is unknown, but genetic and cytological data suggest that it might be linked to spatial organization of the tRNA genes in the nucleus. The early pre-tRNA processing pathway and most tRNA genes associate with the nucleolus in yeast (9, 10), and tgm silencing is released by a mutation affecting nucleolar rRNA processing (6).To explore the mechanism of tgm silencing we have examined its relationship to other silencing forms and its dependence on nucleolar localization. MATERIALS AND METHODSYeast Strains and Genetic Manipulations-The strains used for screening gene deletions is BY4741 (MATa his3⌬1 leu2⌬0 met15⌬0 ura3⌬0 GAL4 GAL80) and its derivatives, ResGen Invitrogen Corp. (Carlsbad, CA). Deletions affecting tgm silencing were confirmed by PCR. Growth on selective media was performed by standard methods except that the G418 concentration in kanamycin selections was doubled (11).Identification of Silencing Suppressors-The deleted gene strains with plasmid pSUP4o (4) were plated on four different syntheti...

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Silencing in Yeast rDNA Chromatin

Cited by 75 publications

References 40 publications

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

Repeat expansion in the budding yeast ribosomal DNA can occur independently of the canonical homologous recombination machinery

Silencing Near tRNA Genes Requires Nucleolar Localization

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