New alleles of SIR2 define cell-cycle-specific silencing functions

Genetics

Volumn 173, Issue 4, 2006, Pages 1939-1950

  Matecic, Mirela ^a,c   Martins Taylor, Kristen ^a   Hickman, Merrit ^a,d   Tanny, Jason ^b,e   Moazed, Danesh ^b   Holmes, Scott G ^a  

^a WESLEYAN UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF VIRGINIA   (United States)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

^e ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; PROTEIN SIR4; SILENT INFORMATION REGULATOR PROTEIN 2; UNCLASSIFIED DRUG;

ALLELE; ARTICLE; CELL CYCLE; CELL CYCLE G1 PHASE; CELL CYCLE G2 PHASE; CELL CYCLE M PHASE; CELL CYCLE PROGRESSION; CHROMATIN STRUCTURE; CONTROLLED STUDY; ENZYME ACTIVITY; GENE LOCUS; GENE SILENCING; HETEROCHROMATIN; IN VIVO STUDY; MITOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; TEMPERATURE SENSITIVITY; YEAST;

ALLELES; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENE EXPRESSION REGULATION, FUNGAL; GENE SILENCING; HEAT; HISTONE DEACETYLASES; MITOSIS; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; SIRTUINS;

EID: 33747865421     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.055491     Document Type: Article

References (63)

1. AFSHAR, G., and J. P. MURNANE, 1999 Characterization of a human gene with sequence homology to Saccharomyces cerevisiae SIR2. Gene 234: 161-168.
2. APARICIO, O. M., and D. E. GOTTSCHLING, 1994 Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Genes Dev. 8: 1133-1146.
3. BEDALOV, A., T. GATBONTON, W. P. IRVINE, D. E. GOTTSCHLING and J. A. SIMON, 2001 Identification of a small molecule inhibitor of Sir2p. Proc. Natl. Acad. Sci. USA 98: 15113-15118.
4. BRACHMANN, C. B., J. M. SHERMAN, S. E. DEVINE, E. E. CAMERON, L. PILLUS et al., 1995 The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes Dev. 9: 2888-2902.
5. BRAUNSTEIN, M., A. B. ROSE, S. G. HOLMES, C. D. ALLIS and J. R. BROACH, 1993 Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev. 7: 592-604.
6. BRAUNSTEIN, M., R. E. SOBEL, C. D. ALLIS, B. M. TURNER and J. R. BROACH, 1996 Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol. Cell. Biol. 16: 4349-4356.
7. BRYK, M., S. D. BRIGGS, B. D. STRAHL, M. J. CURCIO, C. D. ALLIS et al., 2002 Evidence that Set1, a factor required for methylation of histone H3, regulates rDNA silencing in S. cerevisiae by a Sir2-independent mechanism. Curr. Biol. 12: 165-170.
8. BUCK, S. W., J. J. SANDMEIER and J. S. SMITH, 2002 RNA polymerase I propagates unidirectional spreading of rDNA silent chromatin. Cell 111: 1003-1014.
9. CARMEN, A. A., L. MILNE and M. GRUNSTEIN, 2002 Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. J. Biol. Chem. 277: 4778-4781.
10. CHANG, J. F., B. E. HALL, J. C. TANNY, D. MOAZED, D. FILMAN et al., 2003 Structure of the coiled-coil dimerization motif of Sir4 and its interaction with Sir3. Structure 11: 637-649.
11. CHI, M.-H., and D. SHORE, 1996 SUM1-1, a dominant suppressor of SIR mutations in Saccharomyces cerevisiae, increases transcriptional silencing at telomeres and HM mating-type loci and decreases chromosome stability. Mol. Cell. Biol. 16: 4281-4294.
12. COCKELL, M. M., S. PERROD and S. M. GASSER, 2000 Analysis of Sir2p domains required for rDNA and telomeric silencing in Saccharomyces cerevisiae. Genetics 154: 1069-1083.
13. CUBIZOLLES, F., F. MARTINO, S. PERROD and S. M. GASSER, 2006 A homotrimer-heterotrimer switch in Sir2 structure differentiates rDNA and telomeric silencing. Mol. Cell 21: 825-836.
14. DULA, M. L., and S. G. HOLMES, 2000 MGA2 and SPT23 are modifiers of transcriptional silencing in yeast. Genetics 156: 933-941.
15. FOX, C., A. EHRENHOFER-MURRAY, S. LOO and J. RINE, 1997 The origin recognition complex, SIR1, and the S phase requirement for silencing. Science 276: 1547-1551.
16. FRYE, R. A., 2000 Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem. Biophys. Res. Commun. 273: 793-798.
17. GOLDSTEIN, A. L., and J. H. MCCUSKER, 1999 Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15: 1541-1553.
18. HECHT, A., T. LAROCHE, S. STRAHL-BOLSINGER, S. M. GASSER and M. Grunstein, 1995 Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell 80: 583-592.
19. HOLMES, S. G., and J. R. BROACH, 1996 Silencers are required for inheritance of the repressed state in yeast. Genes Dev. 10: 1021-1032.
20. HOPPE, G. J., J. C. TANNY, A. D. RUDNER, S. A. GERBER, S. DANAIE et al., 2002 Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol. Cell. Biol. 22: 4167-4180.
21. HUANG, Y., 2002 Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Nucleic Acids Res. 30: 1465-1482.
22. IMAI, S., C. M. ARMSTRONG, M. KAEBERLEIN and L. GUARENTE, 2000 Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403: 795-800.
23. JAMES, P., J. HALLADAY and E. A. CRAIG, 1996 Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144: 1425-1436.
24. KIRCHMAIER, A. L., and J. RINE, 2001 DNA replication-independent silencing in S. cerevisiae. Science 291: 646-650.
25. KIRCHMAIER, A. L., and J. RINE, 2006 Cell cycle requirements in assembling silent chromatin in Saccharomyces cerevisiae. Mol. Cell. Biol. 26: 852-862.
26. KLAR, A. J., J. N. STRATHERN, J. R. BROACH and J. B. HICKS, 1981 Regulation of transcription in expressed and unexpressed mating type cassettes of yeast. Nature 289: 239-244.
27. LANDRY, J., J. T. SLAMA and R. STERNGLANZ, 2000a Role of NAD(+) in the deacetylase activity of the SIR2-like proteins. Biochem. Biophys. Res. Commun. 278: 685-690.
28. LANDRY, J., A. SUTTON, S. T. TAFROV, R. C. HELLER, J. STEBBINS et al., 2000b The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc. Natl. Acad. Sci. USA 97: 5807-5811.
29. LAU, A., H. BLITZBLAU and S. P. BELL, 2002 Cell-cycle control of the establishment of mating-type silencing in S. cerevisiae. Genes Dev. 16: 2935-2945.
30. LI, Y. C., T. H. CHENG and M. R. GARTENBERG, 2001 Establishment of transcriptional silencing in the absence of DNA replication. Science 291: 650-653.
31. LIOU, G. G., J. C. TANNY, R. G. KRUGER, T. WALZ and D. MOAZED, 2005 Assembly of the SIR complex and its regulation by O-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 121: 515-527.
32. LUO, K., M. A. VEGA-PALAS and M. GRUNSTEIN, 2002 Rap1-Sir4 binding independent of other Sir, yKu, or histone interactions initiates the assembly of telomeric heterochromatin in yeast. Genes Dev. 16: 1528-1539.
33. MAHONEY, D. J., and J. R. BROACH, 1989 The HML mating-type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers. Mol. Cell. Biol. 9: 4621-4630.
34. MARSHALL, M., D. MAHONEY, A. ROSE, J. B. HICKS and J. R. BROACH, 1987 Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Mol. Cell. Biol. 7: 4441-4452.
35. MARTINS-TAYLOR, K., M. L. DULA and S. G. HOLMES, 2004 Heterochromatin spreading at yeast telomeres occurs in M phase. Genetics 168: 65-75.
36. MATECIC, M., S. STUART and S. G. HOLMES, 2002 SIR2-induced inviability is suppressed by histone H4 overexpression. Genetics 162: 973-976.
37. MICHEL, A. H., B. KORNMANN, K. DUBRANA and D. SHORE, 2005 Spontaneous rDNA copy number variation modulates Sir2 levels and epigenetic gene silencing. Genes Dev. 19: 1199-1210.
38. MILLER, A., and K. NASMYTH, 1984 Role of DNA replication in the repression of silent mating type loci in yeast. Nature 312: 247-251.
39. MOAZED, D., 2001 Enzymatic activities of Sir2 and chromatin silencing. Curr. Opin. Cell Biol. 13: 232-238.
40. MOAZED, D., A. KISTLER, A. AXELROD, J. RINE and A. JOHNSON, 1997 Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc. Natl. Acad. Sci. USA 94: 2186-2191.
41. MORETTI, P., K. FREEMAN, L. COODLY and D. SHORE, 1994 Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev. 8: 2257-2269.
42. MUHLRAD, D., R. HUNTER and R. PARKER, 1992 A rapid method for localized mutagenesis of yeast genes. Yeast 8: 79-82.
43. NASMYTH, K. A., K. TATCHELL, B. D. HALL, C. ASTELL and M. SMITH, 1981 A position effect in the control of transcription at yeast mating type loci. Nature 289: 244-250.
44. PAPACS, L. A., Y. SUN, E. L. ANDERSON, J. SUN and S. G. HOLMES, 2004 REP3-mediated silencing in Saccharomyces cerevisiae. Genetics 166: 79-87.
45. PUIG, O., F. CASPARY, G. RIGAUT, B. RUTZ, E. BOUVERET et al., 2001 The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24: 218-229.
46. RIGAUT, G., A. SHEVCHENKO, B. RUTZ, M. WILM, M. MANN et al., 1999 A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17: 1030-1032.
47. RUSCHE, L. N., A. L. KIRCHMAIER and J. RINE, 2002 Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell 13: 2207-2222.
48. RUSCHE, L. N., A. L. KIRCHMAIER and J. RINE, 2003 The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu. Rev. Biochem. 27: 481-516.
49. SHOU, W., J. H. SEOL, A. SHEVCHENKO, C. BASKERVILLE, D. MOAZED et al., 1999 Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex. Cell 97: 233-244.
50. SIKORSKI, R., and P. HIETER, 1989 A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
51. SILICIANO, P. G., and K. TATCHELL, 1984 Transcription and regulatory signals at the mating type locus in yeast. Cell 37: 969-978.
52. SMITH, J. S., C. B. BRACHMANN, I. CELIC, M. A. KENNA, S. MUHAMMAD et al., 2000 A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl. Acad. Sci. USA 97: 6658-6663.
53. SMITH, J. S., J. AVALOS, I. CELIC, S. MUHAMMAD, C. WOLBERGER et al., 2002 SIR2 family of NAD(+)-dependent protein deacetylases. Methods Enzymol. 353: 282-300.
54. STONE, E. M., M. J. SWANSON, A. M. ROMEO, J. B. HICKS and R. STERNGLANZ, 1991 The SIR1 gene of Saccharomyces cerevisiae and its role as an extragenic suppressor of several mating-defective mutants. Mol. Cell. Biol. 11: 2253-2262.
55. STRAIGHT, A. F., W. SHOU, G. J. DOWD, C. W. TURCK, R. J. DESHAIES et al., 1999 Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97: 245-256.
56. SUTER, B., A. TONG, M. CHANG, L. YU, G. W. BROWN et al., 2004 The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae. Genetics 167: 579-591.
57. TANNER, K. G., J. LANDRY, R. STERNGLANZ and J. M. DENU, 2000 Silent information regulator 2 family of NAD-dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose. Proc. Natl. Acad. Sci. USA 97: 14178-14182.
58. TANNY, J. C., and D. MOAZED, 2001 Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: evidence for acetyl transfer from substrate to an NAD breakdown product. Proc. Natl. Acad. Sci. USA 98: 415-420.
59. TANNY, J. C., G. J. DOWD, J. HUANG, H. HILZ and D. MOAZED, 1999 An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99: 735-745.
60. TANNY, J. C., D. S. KIRKPATRICK, S. A. GERBER, S. P. GYGI and D. Moazed, 2004 Budding yeast silencing complexes and regulation of Sir2 activity by protein-protein interactions. Mol. Cell. Biol. 24: 6931-6946.
61. TOBY, G. G., and E. A. GOLEMIS, 2001 Using the yeast interaction trap and other two-hybrid-based approaches to study protein-protein interactions. Methods 24: 201-217.
62. UETZ, P., L. GIOT, G. CAGNEY, T. A. MANSFIELD, R. S. JUDSON et al., 2000 A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
63. WYRICK, J. J., F. C. P. HOLSTEGE, E. G. JENNINGS, H. C. CAUSTON, D. SHORE et al., 1999 Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402: 418-421.