Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast.

Buck, Stephen W.; Shore, David

doi:10.1101/gad.9.3.370

Cited by 193 publications

(171 citation statements)

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“…The dynamic nature of S. cerevisiae silent chromatin suggested by the rapid turnover of Sir4 reported here is consistent with the dynamic nature of HP1 association with heterochromatin in mammalian cells, and the transient association of HP1 or other components of silent chromatin may in turn be regulated by proteolysis. Proper stoichiometry of silent chromatin components is critical for the silenced state (62), with overexpression of Sir proteins or other silencing factors causing reduced silencing (10,37,43,(63)(64)(65). The function for Sir4 instability is unknown, but the ability to combine changes in Sir4 half-life with changes in the activities of other regulators of silent chromatin could provide a rapid mechanism for controlling the establishment or maintenance of the silenced state.…”

Section: Discussionmentioning

confidence: 99%

Sir Antagonist 1 (San1) Is a Ubiquitin Ligase

Dasgupta

Ramsey

Smith

et al. 2004

Journal of Biological Chemistry

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Mutations in Sir Antagonist 1 (SAN1) suppress defects in SIR4 and SPT16 in Saccharomyces cerevisiae. San1 contains a RING domain, suggesting that it functions by targeting mutant sir4 and spt16 proteins for degradation by a ubiquitin-mediated pathway. Consistent with this idea, mutant sir4 and spt16 proteins are unstable in SAN1 cells but are stabilized in san1⌬ cells. We demonstrate that San1 possesses ubiquitin-protein isopeptide ligase activity in vitro, and the ubiquitin-protein isopeptide ligase activity of San1 is required for its function in vivo. Wild-type Sir4 has a half-life of about 21 min, and san1⌬ increased Sir4 half-life to >90 min. In contrast, san1⌬ did not affect the stability of wild-type Spt16, Sir3, Sir2, or the Spt16-associated proteins Pob3 and Nhp6. Loss of SAN1 also did not affect the stability of Ste6-166, a highly unstable protein in yeast. These results support the idea that San1 controls the turnover of a specific class of unstable nuclear proteins. Sir4 nucleates the assembly of silent chromatin at telomeres and the silent mating-type loci (HM) in S. cerevisiae. Sir4 can also affect silencing in the rDNA indirectly by sequestering limiting Sir2. Increasing the stability of wild-type Sir4 by deleting SAN1 had only subtle effects on silencing, suggesting that silent chromatin in yeast is robustly buffered against changes in Sir4 stability. Consistent with the idea that San1 participates as an accessory factor to regulate silent chromatin, including the silent mating-type loci, microarray analysis defined a small but statistically significant role for San1 in transcription of several mating pheromone-responsive genes.

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Section: Discussionmentioning

confidence: 99%

Sir Antagonist 1 (San1) Is a Ubiquitin Ligase

Dasgupta

Ramsey

Smith

et al. 2004

Journal of Biological Chemistry

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“…Telomeric chromatin is thought to act as a "reservoir" of DNA damage response factors, as well as factors that silence rDNA (Kennedy et al, 1997;Smith et al, 1998) and silent mating type loci (Buck and Shore, 1995;Marcand et al, 1996). Telomeric sequestration of telomerase could serve to prevent accidental de novo telomeric DNA addition onto inappropriate DNA substrates such as double-strand breaks, preventing potentially promiscuous and detrimental chromosome "mishealing" events at nontelomeric breaks (Jager and Philippsen, 1989).…”

Section: A Model For Cell Cycle Regulation Of Telomeric Chromatinmentioning

confidence: 99%

Telomeric Protein Distributions and Remodeling Through the Cell Cycle inSaccharomyces cerevisiae

Smith

DeRisi

et al. 2003

MBoC

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In Saccharomyces cerevisiae, telomeric DNA is protected by a nonnucleosomal protein complex, tethered by the protein Rap1. Rif and Sir proteins, which interact with Rap1p, are thought to have further interactions with conventional nucleosomic chromatin to create a repressive structure that protects the chromosome end. We showed by microarray analysis that Rif1p association with the chromosome ends extends to subtelomeric regions many kilobases internal to the terminal telomeric repeats and correlates strongly with the previously determined genomic footprints of Rap1p and the Sir2-4 proteins in these regions. Although the end-protection function of telomeres is essential for genomic stability, telomeric DNA must also be copied by the conventional DNA replication machinery and replenished by telomerase, suggesting that transient remodeling of the telomeric chromatin might result in distinct protein complexes at different stages of the cell cycle. Using chromatin immunoprecipitation, we monitored the association of Rap1p, Rif1p, Rif2p, and the protein component of telomerase, Est2p, with telomeric DNA through the cell cycle. We provide evidence for dynamic remodeling of these components at telomeres. INTRODUCTIONTelomeres are nonnucleosomal protein-DNA complexes that prevent uncontrolled fusion, degradation, recombination, and elongation of chromosome ends (Muller, 1938;McClintock, 1941;Wright et al., 1992;Sandell and Zakian, 1993;Hande et al., 1999;Smith and Blackburn, 1999;Hackett et al., 2001). In Saccharomyces cerevisiae, terminal telomeric DNA is composed of ϳ350 base pairs of short, degenerate TG 1-3 repeats. One telomeric strand is polymerized by telomerase (Cohn and Blackburn, 1995) and forms an S-phasespecific TG 1-3 overhang (Wellinger et al., 1993(Wellinger et al., , 1996. The conventional DNA polymerase machinery is thought to synthesize the complementary C 1-3 A strand. Duplex telomeric DNA repeats are bound by the sequence-specific binding protein Rap1p, which recruits proteins Rif1p and Rif2p as well as Sir3p and Sir4p via its C-terminal domain (Moretti et al., 1994;Moazed and Johnson, 1996;Moretti and Shore, 2001).Telomeric regions in yeast also contain subtelomeric X-elements, which have only moderate homology to each other and are present at all chromosome ends, and the highly homologous YЈ elements located distal to the X elements (Chan and Tye, 1983) on about half of all chromosome ends. YЈ elements fall into 5.2-and 6.7-kb size classes (Louis and Haber, 1990;Louis and Haber, 1992), encode a helicase (Yamada et al., 1998), and are bounded by short (Ͻ150-base pair) tracts of internal telomeric TG 1-3 sequence DNA. Because YЈ elements often occur in tandem arrays of two to four repeats, these TG 1-3 tracts are found internal to the chromosome ends at distances depending upon the size class and number of YЈ elements present.The Rap1p, Ku, and Sir2-4 proteins are cross-linkable to DNA as far in as 3-15 kb from the chromosome end, consistent with their simultaneous binding to TG [1][2][3] repeat DNA ...

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“…Thus, Rif1 attenuates telomeric silencing by competing with Sir complexes for binding to Rap1. Because Sir complexes are limiting, increases in Sir complexes at telomeres are balanced by reductions in Sir complexes at the HM loci (27). Therefore, deletion of RIF1 enhances telomeric silencing and simultaneously reduces HM silencing.…”

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confidence: 99%

Palmitoylation controls the dynamics of budding-yeast heterochromatin via the telomere-binding protein Rif1

Park¹,

Patterson

Cobb³

et al. 2011

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

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The posttranslational addition of palmitate to cysteines occurs ubiquitously in eukaryotic cells, where it functions in anchoring target proteins to membranes and in vesicular trafficking. Here we show that the Saccharomyces cerevisiae palmitoyltransferase Pfa4 enhanced heterochromatin formation at the cryptic mating-type loci HMR and HML via Rif1, a telomere regulatory protein. Acylated Rif1 was detected in extracts from wild-type but not pfa4Δ mutant cells. In a pfa4Δ mutant, Rif1-GFP dispersed away from foci positioned at the nuclear periphery into the nucleoplasm. Sir3-GFP distribution was also perturbed, indicating a change in the nuclear dynamics of heterochromatin proteins. Genetic analyses indicated that PFA4 functioned upstream of RIF1. Surprisingly, the pfa4Δ mutation had only mild effects on telomeric regulation, suggesting Rif1's roles at HM loci and telomeres were more complexly related than previously thought. These data supported a model in which Pfa4-dependent palmitoylation of Rif1 anchored it to the inner nuclear membrane, influencing its role in heterochromatin dynamics.transcriptional silencing | chromosome architecture

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Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast.

Cited by 193 publications

References 46 publications

Sir Antagonist 1 (San1) Is a Ubiquitin Ligase

Sir Antagonist 1 (San1) Is a Ubiquitin Ligase

Telomeric Protein Distributions and Remodeling Through the Cell Cycle inSaccharomyces cerevisiae

Palmitoylation controls the dynamics of budding-yeast heterochromatin via the telomere-binding protein Rif1

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