Abstract
Silencing at native yeast telomeres, in which the subtelomeric elements are intact, is different from silencing at terminal truncations. The repression of URA3 inserted in different subtelomeric positions at several chromosome ends was investigated. Many ends exhibit very little silencing close to the telomere, while others exhibit substantial repression in limited domains. Silencing at native ends is discontinuous, with maximal repression found adjacent to the ARS consensus sequence in the subtelomeric core X element. The level of repression declines precipitously towards the centromere. Mutation of the ARS sequence or an adjacent Abf1p-binding site significantly reduces silencing. The subtelomeric Y' elements are resistant to silencing along their whole length, yet silencing can be re-established at the proximal X element. Deletion of PPR1, the transactivator of URA3, and SIR3 overexpression do not increase repression or extend spreading of silencing to the same extent as with terminally truncated ends. sir1Delta causes partial derepression at X-ACS, in contrast to the lack of effect seen at terminal truncations. orc2-1 and orc5-1 have no effect on natural silencing yet cause derepression at truncated ends. X-ACS silencing requires the proximity of the telomere and is dependent on SIR2, SIR3, SIR4 and HDF1. The structures found at native yeast telomeres appear to limit the potential of repressive chromatin.
Full Text
The Full Text of this article is available as a PDF (521.8 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Aparicio O. M., Billington B. L., Gottschling D. E. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell. 1991 Sep 20;66(6):1279–1287. doi: 10.1016/0092-8674(91)90049-5. [DOI] [PubMed] [Google Scholar]
- Aparicio O. M., Gottschling D. E. Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Genes Dev. 1994 May 15;8(10):1133–1146. doi: 10.1101/gad.8.10.1133. [DOI] [PubMed] [Google Scholar]
- Baudin A., Ozier-Kalogeropoulos O., Denouel A., Lacroute F., Cullin C. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 1993 Jul 11;21(14):3329–3330. doi: 10.1093/nar/21.14.3329. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Blue C., Marcand S., Gilson E. Proteins that bind to double-stranded regions of telomeric DNA. Trends Cell Biol. 1997 Aug;7(8):317–324. doi: 10.1016/S0962-8924(97)01092-1. [DOI] [PubMed] [Google Scholar]
- Boeke J. D., LaCroute F., Fink G. R. A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol Gen Genet. 1984;197(2):345–346. doi: 10.1007/BF00330984. [DOI] [PubMed] [Google Scholar]
- Borts R. H., Lichten M., Haber J. E. Analysis of meiosis-defective mutations in yeast by physical monitoring of recombination. Genetics. 1986 Jul;113(3):551–567. doi: 10.1093/genetics/113.3.551. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Boulton S. J., Jackson S. P. Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing. EMBO J. 1998 Mar 16;17(6):1819–1828. doi: 10.1093/emboj/17.6.1819. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chien C. T., Buck S., Sternglanz R., Shore D. Targeting of SIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell. 1993 Nov 5;75(3):531–541. doi: 10.1016/0092-8674(93)90387-6. [DOI] [PubMed] [Google Scholar]
- Dillin A., Rine J. Separable functions of ORC5 in replication initiation and silencing in Saccharomyces cerevisiae. Genetics. 1997 Nov;147(3):1053–1062. doi: 10.1093/genetics/147.3.1053. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Enomoto S., Longtine M. S., Berman J. Enhancement of telomere-plasmid segregation by the X-telomere associated sequence in Saccharomyces cerevisiae involves SIR2, SIR3, SIR4 and ABF1. Genetics. 1994 Mar;136(3):757–767. doi: 10.1093/genetics/136.3.757. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fourel G., Revardel E., Koering C. E., Gilson E. Cohabitation of insulators and silencing elements in yeast subtelomeric regions. EMBO J. 1999 May 4;18(9):2522–2537. doi: 10.1093/emboj/18.9.2522. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fox C. A., Ehrenhofer-Murray A. E., Loo S., Rine J. The origin recognition complex, SIR1, and the S phase requirement for silencing. Science. 1997 Jun 6;276(5318):1547–1551. doi: 10.1126/science.276.5318.1547. [DOI] [PubMed] [Google Scholar]
- Fox C. A., Loo S., Dillin A., Rine J. The origin recognition complex has essential functions in transcriptional silencing and chromosomal replication. Genes Dev. 1995 Apr 15;9(8):911–924. doi: 10.1101/gad.9.8.911. [DOI] [PubMed] [Google Scholar]
- Gietz D., St Jean A., Woods R. A., Schiestl R. H. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 1992 Mar 25;20(6):1425–1425. doi: 10.1093/nar/20.6.1425. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gotta M., Strahl-Bolsinger S., Renauld H., Laroche T., Kennedy B. K., Grunstein M., Gasser S. M. Localization of Sir2p: the nucleolus as a compartment for silent information regulators. EMBO J. 1997 Jun 2;16(11):3243–3255. doi: 10.1093/emboj/16.11.3243. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gottschling D. E., Aparicio O. M., Billington B. L., Zakian V. A. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell. 1990 Nov 16;63(4):751–762. doi: 10.1016/0092-8674(90)90141-z. [DOI] [PubMed] [Google Scholar]
- Gravel S., Larrivée M., Labrecque P., Wellinger R. J. Yeast Ku as a regulator of chromosomal DNA end structure. Science. 1998 May 1;280(5364):741–744. doi: 10.1126/science.280.5364.741. [DOI] [PubMed] [Google Scholar]
- Grunstein M. Molecular model for telomeric heterochromatin in yeast. Curr Opin Cell Biol. 1997 Jun;9(3):383–387. doi: 10.1016/s0955-0674(97)80011-7. [DOI] [PubMed] [Google Scholar]
- Grunstein M. Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell. 1998 May 1;93(3):325–328. doi: 10.1016/s0092-8674(00)81160-5. [DOI] [PubMed] [Google Scholar]
- Hecht A., Strahl-Bolsinger S., Grunstein M. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature. 1996 Sep 5;383(6595):92–96. doi: 10.1038/383092a0. [DOI] [PubMed] [Google Scholar]
- Larin Z., Monaco A. P., Lehrach H. Generation of large insert YAC libraries. Methods Mol Biol. 1996;54:1–11. doi: 10.1385/0-89603-313-9:1. [DOI] [PubMed] [Google Scholar]
- Laroche T., Martin S. G., Gotta M., Gorham H. C., Pryde F. E., Louis E. J., Gasser S. M. Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres. Curr Biol. 1998 May 21;8(11):653–656. doi: 10.1016/s0960-9822(98)70252-0. [DOI] [PubMed] [Google Scholar]
- Loo S., Rine J. Silencing and heritable domains of gene expression. Annu Rev Cell Dev Biol. 1995;11:519–548. doi: 10.1146/annurev.cb.11.110195.002511. [DOI] [PubMed] [Google Scholar]
- Louis E. J., Haber J. E. Evolutionarily recent transfer of a group I mitochondrial intron to telomere regions in Saccharomyces cerevisiae. Curr Genet. 1991 Nov;20(5):411–415. doi: 10.1007/BF00317070. [DOI] [PubMed] [Google Scholar]
- Louis E. J., Haber J. E. Mitotic recombination among subtelomeric Y' repeats in Saccharomyces cerevisiae. Genetics. 1990 Mar;124(3):547–559. doi: 10.1093/genetics/124.3.547. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Louis E. J., Naumova E. S., Lee A., Naumov G., Haber J. E. The chromosome end in yeast: its mosaic nature and influence on recombinational dynamics. Genetics. 1994 Mar;136(3):789–802. doi: 10.1093/genetics/136.3.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Louis E. J. The chromosome ends of Saccharomyces cerevisiae. Yeast. 1995 Dec;11(16):1553–1573. doi: 10.1002/yea.320111604. [DOI] [PubMed] [Google Scholar]
- Lustig A. J. Mechanisms of silencing in Saccharomyces cerevisiae. Curr Opin Genet Dev. 1998 Apr;8(2):233–239. doi: 10.1016/s0959-437x(98)80146-9. [DOI] [PubMed] [Google Scholar]
- Nugent C. I., Bosco G., Ross L. O., Evans S. K., Salinger A. P., Moore J. K., Haber J. E., Lundblad V. Telomere maintenance is dependent on activities required for end repair of double-strand breaks. Curr Biol. 1998 May 21;8(11):657–660. doi: 10.1016/s0960-9822(98)70253-2. [DOI] [PubMed] [Google Scholar]
- Pirrotta V. Chromatin-silencing mechanisms in Drosophila maintain patterns of gene expression. Trends Genet. 1997 Aug;13(8):314–318. doi: 10.1016/s0168-9525(97)01178-5. [DOI] [PubMed] [Google Scholar]
- Polotnianka R. M., Li J., Lustig A. J. The yeast Ku heterodimer is essential for protection of the telomere against nucleolytic and recombinational activities. Curr Biol. 1998 Jul 2;8(14):831–834. doi: 10.1016/s0960-9822(98)70325-2. [DOI] [PubMed] [Google Scholar]
- Porter S. E., Greenwell P. W., Ritchie K. B., Petes T. D. The DNA-binding protein Hdf1p (a putative Ku homologue) is required for maintaining normal telomere length in Saccharomyces cerevisiae. Nucleic Acids Res. 1996 Feb 15;24(4):582–585. doi: 10.1093/nar/24.4.582. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pryde F. E., Huckle T. C., Louis E. J. Sequence analysis of the right end of chromosome XV in Saccharomyces cerevisiae: an insight into the structural and functional significance of sub-telomeric repeat sequences. Yeast. 1995 Apr 15;11(4):371–382. doi: 10.1002/yea.320110410. [DOI] [PubMed] [Google Scholar]
- Pryde F. E., Louis E. J. Saccharomyces cerevisiae telomeres. A review. Biochemistry (Mosc) 1997 Nov;62(11):1232–1241. [PubMed] [Google Scholar]
- Renauld H., Aparicio O. M., Zierath P. D., Billington B. L., Chhablani S. K., Gottschling D. E. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. Genes Dev. 1993 Jul;7(7A):1133–1145. doi: 10.1101/gad.7.7a.1133. [DOI] [PubMed] [Google Scholar]
- Rine J., Herskowitz I. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics. 1987 May;116(1):9–22. doi: 10.1093/genetics/116.1.9. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rine J., Strathern J. N., Hicks J. B., Herskowitz I. A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: evidence for and identification of cryptic mating-type loci. Genetics. 1979 Dec;93(4):877–901. doi: 10.1093/genetics/93.4.877. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Runge K. W., Zakian V. A. Introduction of extra telomeric DNA sequences into Saccharomyces cerevisiae results in telomere elongation. Mol Cell Biol. 1989 Apr;9(4):1488–1497. doi: 10.1128/mcb.9.4.1488. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sherman J. M., Pillus L. An uncertain silence. Trends Genet. 1997 Aug;13(8):308–313. doi: 10.1016/s0168-9525(97)01198-0. [DOI] [PubMed] [Google Scholar]
- Strahl-Bolsinger S., Hecht A., Luo K., Grunstein M. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 1997 Jan 1;11(1):83–93. doi: 10.1101/gad.11.1.83. [DOI] [PubMed] [Google Scholar]
- Triolo T., Sternglanz R. Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. Nature. 1996 May 16;381(6579):251–253. doi: 10.1038/381251a0. [DOI] [PubMed] [Google Scholar]
- Vega-Palas M. A., Venditti S., Di Mauro E. Heterochromatin organization of a natural yeast telomere. Changes of nucleosome distribution driven by the absence of Sir3p. J Biol Chem. 1998 Apr 17;273(16):9388–9392. doi: 10.1074/jbc.273.16.9388. [DOI] [PubMed] [Google Scholar]
- Vega-Palas M. A., Venditti S., Di Mauro E. Telomeric transcriptional silencing in a natural context. Nat Genet. 1997 Mar;15(3):232–233. doi: 10.1038/ng0397-232. [DOI] [PubMed] [Google Scholar]
- Wach A., Brachat A., Pöhlmann R., Philippsen P. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast. 1994 Dec;10(13):1793–1808. doi: 10.1002/yea.320101310. [DOI] [PubMed] [Google Scholar]
- Wotton D., Shore D. A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae. Genes Dev. 1997 Mar 15;11(6):748–760. doi: 10.1101/gad.11.6.748. [DOI] [PubMed] [Google Scholar]
- Zou S., Ke N., Kim J. M., Voytas D. F. The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes Dev. 1996 Mar 1;10(5):634–645. doi: 10.1101/gad.10.5.634. [DOI] [PubMed] [Google Scholar]