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. 2012 Aug 2:3:144.
doi: 10.3389/fgene.2012.00144. eCollection 2012.

Effects of Perinuclear Chromosome Tethers in the Telomeric URA3/5FOA System Reflect Changes to Gene Silencing and not Nucleotide Metabolism

Affiliations

Effects of Perinuclear Chromosome Tethers in the Telomeric URA3/5FOA System Reflect Changes to Gene Silencing and not Nucleotide Metabolism

Betty P K Poon et al. Front Genet. .

Abstract

Telomeres are repetitive DNA sequences that protect the ends of linear chromosomes. Telomeres also recruit histone deacetylase complexes that can then spread along chromosome arms and repress the expression of subtelomeric genes in a process known as telomere position effect (TPE). In the budding yeast Saccharomyces cerevisiae, association of telomeres with the nuclear envelope is thought to promote TPE by increasing the local concentration of histone deacetylase complexes at chromosome ends. Importantly, our understanding of TPE stems primarily from studies that employed marker genes inserted within yeast subtelomeres. In particular, the prototrophic marker URA3 is commonly used to assay TPE by negative selection on media supplemented with 5-fluoro-orotic acid (5FOA). Recent findings suggested that decreased growth on 5FOA-containing media may not always indicate increased expression of a telomeric URA3 reporter, but can rather reflect an increase in ribonucleotide reductase (RNR) function and nucleotide metabolism. Thus, we set out to test if the 5FOA sensitivity of subtelomeric URA3-harboring cells in which we deleted various factors implicated in perinuclear telomere tethering reflects changes to TPE and/or RNR. We report that RNR inhibition restores 5FOA resistance to cells lacking RNR regulatory factors but not any of the major telomere tethering and silencing factors, including Sir2, cohibin, Mps3, Heh1, and Esc1. In addition, we find that the disruption of tethering pathways in which these factors participate increases the level of URA3 transcripts originating from the telomeric reporter gene and abrogates silencing of subtelomeric HIS3 reporter genes without altering RNR gene expression. Thus, increased 5FOA sensitivity of telomeric URA3-harboring cells deficient in telomere tethers reflects the dysregulation of TPE but not RNR. This is key to understanding relationships between telomere positioning, chromatin silencing, and lifespan.

Keywords: Esc1; Heh1; Mps3; SIR; URA3/5FOA; cohibin; ribonucleotide reductase; telomere position effect.

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Figures

Figure 1
Figure 1
Cohibin is required for silencing of the telomeric reporter gene HIS3. (A) Schematic of the HIS3 reporter gene inserted proximal to TELVII-L. (B) Serial dilutions of cells with the telomeric HIS3 reporter were plated on synthetic complete (SC) medium or SC media without histidine (−HIS) and with increasing concentrations of 3-amino-1,2,4-triazole (+3AT; HIS3 silencing inhibits growth). WT, wild-type. Strains: KMY984, KMY986, KMY1303, KMY1307.
Figure 2
Figure 2
Pharmacological inhibition of RNR function restores FOA-resistance in cac1Δ cells but not Sir2- or cohibin-deficient cells harboring a telomeric URA3 reporter gene. (A) Schematic of the URA3 reporter gene inserted proximal to TELVII-L. (B,C) Serial dilutions of cells with the telomeric URA3 reporter were plated on synthetic complete (SC) medium or medium supplemented with sublethal concentrations of hydroxyurea (+HU) and/or 5FOA (+5FOA). WT, wild-type. Strains: KMY368, KMY416, KMY1465, KMY74, KMY77.
Figure 3
Figure 3
FOA-treatment increases RNR expression in dot1Δ and cac1Δ cells, but not lrs4Δ cells, and CDC21 overexpression or HU treatment restores 5FOA resistance to dot1Δ and cac1Δ cells, but not lrs4Δ cells. (A) RNR4 transcript levels (normalized to ACT1) as measured by quantitative reverse transcriptase PCR (qRT-PCR) following a 4-h treatment with 5FOA or DMSO. Error bars represent the SEM for three independent experiments. WT, wild-type. Strains: KMY368, KMY1391, KMY1465, KMY74, KMY59. (B) Expression levels of RNR4 (normalized to ACT1) measured by qRT-PCR following a 4-h treatment with 5FOA with or without HU. Error bars represent the SEM for two independent experiments. WT, wild-type. Strains: KMY368, KMY1391, KMY1465. (C) Schematic showing impact of 5FOA on RNR in dot1Δ or cac1Δ cells (top). Serial dilutions of cells with the URA3 reporter gene inserted proximal to telomere VII-L were plated on synthetic complete (SC) medium, medium lacking leucine (−LEU), or medium lacking leucine, and supplemented with 5FOA (−LEU + 5FOA; bottom). All cells were spotted on the same corresponding plates. WT, wild-type. Strains: KMY368, KMY1391, KMY1465, KMY74. (D) URA3-TELVII-L transcript levels (normalized to ACT1) as measured by qRT-PCR. Error bars represent the SEM for three independent runs. WT, wild-type. Strains: KMY1565, KMY1567, KMY1568.
Figure 4
Figure 4
Pharmacological inhibition of RNR function does not restore FOA-resistance in cells lacking cohibin-associated/telomere tethering nuclear envelope proteins. (A) Schematic showing relationship between cohibin and the INM proteins Heh1 and Mps3 in perinuclear telomere tethering. (B) Serial dilutions of cells with the URA3 reporter gene inserted proximal to telomere VII-L were plated on synthetic complete (SC) medium or medium supplemented with a sublethal concentration of hydroxyurea (+HU) and/or 5FOA (+5FOA). WT, wild-type. Strains: KMY368, KMY1465, KMY74, KMY59, KMY999, KMY1468, KMY1470. (C) Deletion of LRS4 or HEH1 does not affect mps3Δ75-150 levels as indicated by immunoblotting. A non-specific band served as loading control. All lanes were run and transferred from the same gel. WT, wild-type. Strains: KMY368, KMY999, KMY1467, KMY1468, KMY1469, KMY1470.
Figure 5
Figure 5
Pharmacological inhibition of RNR function does not restore FOA-resistance in cells lacking Esc1 and/or cohibin-dependent telomere tethering. (A) Schematic showing relationship between cohibin-dependent and Esc1-dependent perinuclear telomere tethering. (B) Serial dilutions of cells with the URA3 reporter inserted proximal to telomere VII-L were plated on synthetic complete (SC) medium or medium supplemented with sublethal concentrations of hydroxyurea (+HU) and/or 5FOA (+5FOA). WT, wild-type. Strains: KMY368, KMY1465, KMY74, KMY59, KMY404, KMY492, KMY489.
Figure 6
Figure 6
Perinuclear telomere tethers impact the telomeric URA3/5FOA reporter system as a result of changes to TPE and not nucleotide metabolism. Unlike dot1Δ or cac1Δ cells, RNR expression is unaffected in cells lacking various perinuclear telomere tethering factors including Sir2, cohibin, Esc1, Mps3, and Heh1. In addition, the 5FOA sensitivity of URA3-TELVII-L-harboring cells that lack these telomere-associated factors, but not Dot1/Cac1, is not restored upon RNR inhibition, which can be achieved via defined HU treatments or CDC21 overexpression. Thus, the effects of major telomere tethering factors in telomeric URA3/5FOA reporter systems assaying for TPE reflect changes to chromatin assembly and gene expression but not nucleotide metabolism.

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