A Common Telomeric Gene Silencing Assay Is Affected by Nucleotide Metabolism

Rossmann, Marlies P.; Luo, Weijun; Tsaponina, Olga; Chabes, Andrei; Stillman, Bruce

doi:10.1016/j.molcel.2011.03.007

Cited by 66 publications

(100 citation statements)

References 39 publications

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“…Additionally, some Y9 elements are transcribed, a fact that is inconsistent with Sir protein-mediated repression of all Y9 elements (Fourel et al 1999;Pryde and Louis 1999). In addition to these discrepancies, metabolic reporters are not biologically neutral, and some complexity regarding these reporters has emerged (Rossmann et al 2011;Takahashi et al 2011). For example, DOT1, SWI4, and ARD1, all of which abrogate H3K79 methylation, had been implicated in telomeric silencing, as assayed by the URA3 reporter at artificial telomeres.…”

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The Chromatin and Transcriptional Landscape of NativeSaccharomyces cerevisiaeTelomeres and Subtelomeric Domains

2015

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Saccharomyces cerevisiae telomeres have been a paradigm for studying telomere position effects on gene expression. Telomere position effect was first described in yeast by its effect on the expression of reporter genes inserted adjacent to truncated telomeres. The reporter genes showed variable silencing that depended on the Sir2/3/4 complex. Later studies examining subtelomeric reporter genes inserted at natural telomeres hinted that telomere position effects were less pervasive than previously thought. Additionally, more recent data using the sensitive technology of chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) revealed a discrete and noncontinuous pattern of coenrichment for all three Sir proteins at a few telomeres, calling the generality of these conclusions into question. Here we combined the ChIP-Seq of the Sir proteins with RNA sequencing (RNA-Seq) of messenger RNAs (mRNAs) in wild-type and in SIR2, SIR3, and SIR4 deletion mutants to characterize the chromatin and transcriptional landscape of all native S. cerevisiae telomeres at the highest achievable resolution. Most S. cerevisiae chromosomes had subtelomeric genes that were expressed, with only 6% of subtelomeric genes silenced in a SIR-dependent manner. In addition, we uncovered 29 genes with previously unknown cell-type-specific patterns of expression. These detailed data provided a comprehensive assessment of the chromatin and transcriptional landscape of the subtelomeric domains of a eukaryotic genome.KEYWORDS Sir complex; telomeres; ChIP-Seq; RNA-Seq; mating-type regulation T ELOMERES are specialized structures at the ends of eukaryotic chromosomes that are critical for various biological functions. Telomeres bypass the problem of replicating the ends of linear DNA, protect chromosome ends from exonucleases and nonhomologous end joining, prevent the linear DNA ends from activating a DNA-damage checkpoint, and exhibit suppressed recombination [reviewed in Wellinger and Zakian (2012)]. In Saccharomyces cerevisiae, telomeres are composed of three sequence features: telomeric repeats, which consist of 300 6 75 bp of (TG 1-3 ) n repeated units produced by telomerase; X elements; and Y9 elements, which contain an ORF for a putative helicase gene. The X elements are subdivided into a core X [consisting of an autonomously replicating sequence (ARS) consensus sequence and an Abf1-binding site] and subtelomeric repeats that have variable numbers of repeated units containing a binding site for Tbf1 (Louis 1995). All telomeres contain telomeric repeats plus an X element, and about half of S. cerevisiae's 32 telomeres also contain a Y9 element (X-Y9 telomeres). X-only telomeres contain an X element but not a Y9 element. Unlike the Y9 elements, the telomeric repeats and X elements are bound by proteins that are critical for maintenance of telomeres. Rap1 binds the TG 1-3 telomeric repeats and recruits the Sir2/3/4 protein complex, the trio of heterochromatin structural proteins critical for repression of the silent mating ...

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The Chromatin and Transcriptional Landscape of NativeSaccharomyces cerevisiaeTelomeres and Subtelomeric Domains

2015

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“…It was originally identified as a high copy disruptor of telomeric silencing in Saccharomyces cerevisiae (10). Two recent studies have demonstrated that the role of Dot1 in heterochromatin gene silencing might be overestimated in the original URA3 telomere silencing reporter assays in yeast (11,12). Nevertheless, Dot1 participates in heterochromatin formation through competing with Sir3 for a binding site on histone H4 (13).…”

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A Prototypic Lysine Methyltransferase 4 from Archaea with Degenerate Sequence Specificity Methylates Chromatin Proteins Sul7d and Cren7 in Different Patterns

Niu

Xia

Wang

et al. 2013

Journal of Biological Chemistry

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Background:The origin of eukaryotic histone modification enzymes still remains obscure. Results: Prototypic KMT4/Dot1 from Archaea targets chromatin proteins (Sul7d and Cren7) and shows increased activity on Sul7d, but not Cren7, in the presence of DNA. Conclusion: Promiscuous aKMT4 could be regulated by chromatin environment. Significance: This study supports the prokaryotic origin model of eukaryotic histone methyltransferases and sheds light on chromatin dynamics in Archaea.

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“…1 are metabolic in nature and Gdh1 is a metabolic protein, we further evaluated Gdh1's role in silencing through independent assays. Recent studies showed that 5-FOA-based telomeric silencing assays could give false-positive results for mutants that elevate ribonucleotide reductase (RNR) activities (37,38). One way to eliminate the confounding effect is to inhibit RNR activity with 10 mM hydroxyurea (HU) (37).…”

Section: Gdh1 Regulates Recruitment Of Sir Proteins To Silent Chromatmentioning

confidence: 99%

“…Recent studies showed that 5-FOA-based telomeric silencing assays could give false-positive results for mutants that elevate ribonucleotide reductase (RNR) activities (37,38). One way to eliminate the confounding effect is to inhibit RNR activity with 10 mM hydroxyurea (HU) (37). Adding HU did not rescue the 5-FOA sensitivity of gdh1Δ TELV-R::URA3, suggesting that the 5-FOA readout is likely a true reflection of gdh1Δ's silencing defect ( Fig.…”

Section: Gdh1 Regulates Recruitment Of Sir Proteins To Silent Chromatmentioning

confidence: 99%

Functions for diverse metabolic activities in heterochromatin

Xue

Pillus

2016

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

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Growing evidence demonstrates that metabolism and chromatin dynamics are not separate processes but that they functionally intersect in many ways. For example, the lysine biosynthetic enzyme homocitrate synthase was recently shown to have unexpected functions in DNA damage repair, raising the question of whether other amino acid metabolic enzymes participate in chromatin regulation. Using an in silico screen combined with reporter assays, we discovered that a diverse range of metabolic enzymes function in heterochromatin regulation. Extended analysis of the glutamate dehydrogenase 1 (Gdh1) revealed that it regulates silent information regulator complex recruitment to telomeres and ribosomal DNA. Enhanced N-terminal histone H3 proteolysis is observed in GDH1 mutants, consistent with telomeric silencing defects. A conserved catalytic Asp residue is required for Gdh1's functions in telomeric silencing and H3 clipping. Genetic modulation of α-ketoglutarate levels demonstrates a key regulatory role for this metabolite in telomeric silencing. The metabolic activity of glutamate dehydrogenase thus has important and previously unsuspected roles in regulating chromatin-related processes.I n eukaryotic nuclei, DNA is wrapped around histones to form nucleosomes, the basic subunits of chromatin (1). The physical and chemical properties of chromatin are regulated by at least two types of enzymatic activities: chromatin remodeling and posttranslational modifications of histones and chromatin-associated proteins (2, 3). These enzymatic activities directly determine the accessibility of DNA for transcription, replication, and repair.In Saccharomyces cerevisiae, three genomic regions are known to contain loci repressed by chromatin-related activities. These include the HM silent mating-type loci (HMR and HML), regions within the ribosomal DNA (rDNA), and some telomeres. Transcriptional silencing at these loci is established and maintained by a number of factors, including the Sirtuin class III deacetylase activity of silent information protein 2 (Sir2). Notably, Sir2 uses NAD + as a cofactor to deacetylate histones H3 and H4 in newly deposited nucleosomes. Other than Sir2, the composition of the silencing complexes and the mechanisms of silencing are different for the three silenced regions, with the telomeres and the HM loci more similar to each other and the rDNA locus having distinct features (reviewed in ref. 4). Silencing at telomeres and the HM loci was long considered to follow a sequential model: initial deacetylation by Sir2 creates binding sites for Sir3 and Sir4, which in turn regulate the spreading of Sir2 across these regions (5). More recent high-resolution studies report a less uniform landscape for silenced chromatin (6), although the central importance of the Sir proteins remains clear. They, together with transcription factors including Rap1 and Abf1, form a multisubunit silencing complex known as the silent information regulator (SIR) complex. Silencing at the rDNA locus does not involve the SIR complex but ra...

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A Common Telomeric Gene Silencing Assay Is Affected by Nucleotide Metabolism

Cited by 66 publications

References 39 publications

The Chromatin and Transcriptional Landscape of NativeSaccharomyces cerevisiaeTelomeres and Subtelomeric Domains

The Chromatin and Transcriptional Landscape of NativeSaccharomyces cerevisiaeTelomeres and Subtelomeric Domains

A Prototypic Lysine Methyltransferase 4 from Archaea with Degenerate Sequence Specificity Methylates Chromatin Proteins Sul7d and Cren7 in Different Patterns

Functions for diverse metabolic activities in heterochromatin

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