The molecular topography of silenced chromatin in Saccharomyces cerevisiae

Genes and Development

Volumn 28, Issue 3, 2014, Pages 245-258

  Thurtle, Deborah M ^a   Rine, Jasper ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

ChIP seq; H4K16 acetyl; Heterochromatin; Histones; Sir complex

Indexed keywords

HISTONE; HISTONE H4K16; SILENT INFORMATION REGULATOR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CROSS LINKING; GENE LOCUS; GENE REPRESSION; HETEROCHROMATIN; HISTONE MODIFICATION; MOLECULAR MECHANICS; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; TELOMERE;

CHIP-SEQ; H4K16-ACETYL; HETEROCHROMATIN; HISTONES; SIR COMPLEX;

CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; GENE SILENCING; HISTONES; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; SACCHAROMYCES CEREVISIAE; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; TELOMERE;

EID: 84893453174     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.230532.113     Document Type: Article

References (75)

1. Aparicio O, Geisberg JV, Sekinger E, Yang A, Moqtaderi Z, Struhl K. 2005. Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Mol Biol 23: 17.7.1-17.7.23.
2. Armache KJ, Garlick JD, Canzio D, Narlikar GJ, Kingston RE. 2011. Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 Åresolution. Science 334: 977-982.
3. Bantignies F, Roure V, Comet I, Leblanc B, Schuettengruber B, Bonnet J, Tixier V, Mas A, Cavalli G. 2011. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144: 214-226.
4. Beisel C, Paro R. 2011. Silencing chromatin: Comparing modes and mechanisms. Nat Rev Genet 12: 123-135.
5. Bi X, Braunstein M, Shei G-J, Broach JR. 1999. The yeast HML I silencer defines a heterochromatin domain boundary by directional establishment of silencing. Proc Natl Acad Sci 96: 11934-11939.
6. Brand AH, Breeden L, Abraham J, Sternglanz R, Nasmyth K. 1985. Characterization of a 'silencer' in yeast: A DNA sequence with properties opposite to those of a transcriptional enhancer. Cell 41: 41-48.
7. Chen L, Widom J. 2005. Mechanism of transcriptional silencing in yeast. Cell 120: 37-48.
8. Chen Y, Rai R, Zhou Z-R, Kanoh J, Ribeyre C, Yang Y, Zheng H, Damay P, Wang F, Tsujii H, et al. 2011. A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms. Nat Struct Mol Biol 18: 213-221.
9. Cheng T-H, Gartenberg MR. 2000. Yeast heterochromatin is a dynamic structure that requires silencers continuously. Genes Dev 14: 452-463.
10. Conrad T, Akhtar A. 2012. Dosage compensation in Drosophila melanogaster: Epigenetic fine-tuning of chromosome-wide transcription. Nat Rev Genet 13: 123-134.
11. Dekker J, Rippe K, Dekker M, Kleckner N. 2002. Capturing chromosome conformation. Science 295: 1306-1311.
12. Donze D, Kamakaka RT. 2001. RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J 20: 520-531.
13. Donze D, Adams CR, Rine J, Kamakaka RT. 1999. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev 13: 698-708.
14. Ehrentraut S, Weber JM, Dybowski JN, Hoffmann D, Ehrenhofer-Murray AE. 2010. Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate. Proc Natl Acad Sci 107: 5522-5527.
15. Flores O, Orozco M. 2011. nucleR: A package for non-parametric nucleosome positioning. Bioinformatics 27: 2149-2150.
16. Fourel G, Revardel E, Koering CE, Gilson E. 1999. Cohabitation of insulators and silencing elements in yeast subtelomeric regions. EMBO J 18: 2522-2537.
17. Furuyama S, Biggins S. 2007. Centromere identity is specified by a single centromeric nucleosome in budding yeast. Proc Natl Acad Sci 104: 14706-14711.
18. Gao L, Gross DS. 2008. Sir2 silences gene transcription by targeting the transition between RNA polymerase II initiation and elongation. Mol Cell Biol 28: 3979-3994.
19. Ghidelli S, Donze D, Dhillon N, Kamakaka RT. 2001. Sir2p exists in two nucleosome-binding complexes with distinct deacetylase activities. EMBO J 20: 4522-4535.
20. Gottschling DE, Aparicio OM, Billington BL, Zakian VA. 1990. Position effect at S. cerevisiae telomeres: Reversible repression of Pol II transcription. Cell 63: 751-762.
21. Grunstein M, Gasser SM. 2013. Epigenetics in Saccharomyces cerevisiae. Cold Spring Harb Perspect Biol 5: a017491.
22. Hecht A, Strahl-Bolsinger S, Grunstein M. 1996. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383: 92-96.
23. Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. 2011. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci 108: 18318-18323.
24. Hicks J, Strathern JN, Klar AJS. 1979. Transposable mating type genes in Saccharomyces cerevisiae. Nature 282: 478-483.
25. Hoppe GJ, Tanny JC, Rudner AD, Gerber SA, Danaie S, Gygi SP, Moazed D. 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.
26. Hou Z. 2005. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc Natl Acad Sci 102: 8489-8494.
27. Imai S, Armstrong CM, Kaeberlein M, Guarente L. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403: 795-800.
28. Jeon Y, Sarma K, Lee JT. 2012. New and Xisting regulatory mechanisms of X chromosome inactivation. Curr Opin Genet Dev 22: 62-71.
29. Johnson LM, Kayne PS, Kahn ES, Grunstein M. 1990. Genetic evidence for an interaction between SIR3 and histone H4 in the repression of the silent mating loci in Saccharomyces cerevisiae. Proc Natl Acad Sci 87: 6286-6290.
30. Johnson A, Li G, Sikorski TW, Buratowski S, Woodcock CL, Moazed D. 2009. Reconstitution of heterochromatindependent transcriptional gene silencing. Mol Cell 35: 769-781.
31. Kimura A, Umehara T, Horikoshi M. 2002. Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nat Genet 32: 370-377.
32. Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, Pillus L, Sternglanz R. 2000. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci 97: 5807-5811.
33. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
34. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
35. Li M, Valsakumar V, Poorey K, Bekiranov S, Smith JS. 2013. Genome-wide analysis of functional sirtuin chromatin targets in yeast. Genome Biol 14: R48.
36. Lieb JD, Liu X, Botstein D, Brown PO. 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 303-304.
37. Loney ER, Inglis PW, Sharp S, Pryde FE, Kent NA, Mellor J, Louis EJ. 2009. Repressive and non-repressive chromatin at native telomeres in Saccharomyces cerevisiae. Epigenetics Chromatin 2: 18.
38. Longtine MS, McKenzie A, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14: 953-961.
39. Loo S, Rine J. 1994. Silencers and domains of generalized repression. Science 264: 1768-1771.
40. Louis EJ. 1995. The chromosome ends of Saccharomyces cerevisiae. Yeast 11: 1553-1573.
41. Lynch PJ, Rusche LN. 2008. A silencer promotes the assembly of silenced chromatin independently of recruitment. Mol Cell Biol 29: 43-56.
42. Martino F, Kueng S, Robinson P, Tsai-Pflugfelder M, van Leeuwen F, Ziegler M, Cubizolles F, Cockell MM, Rhodes D, Gasser SM. 2009. Reconstitution of yeast silent chromatin: Multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro. Mol Cell 33: 323-334.
43. Meyer BJ. 2010. Targeting X chromosomes for repression. Curr Opin Genet Dev 20: 179-189.
44. Nasmyth KA, Tatchell K. 1980. The structure of transposable yeast mating type loci. Cell 19: 753-764.
45. Oki M, Kamakaka RT. 2005. Barrier function at HMR. Mol Cell 19: 707-716.
46. Oppikofer M, Kueng S, Martino F, Soeroes S, Hancock SM, Chin JW, Fischle W, Gasser SM. 2011. A dual role of H4K16 acetylation in the establishment of yeast silent chromatin. EMBO J 30: 2610-2621.
47. Park EC, Szostak JW. 1990. Point mutations in the yeast histone H4 gene prevent silencing of the silent mating type locus HML. Mol Cell Biol 10: 4932-4934.
48. Phillips-Cremins JE, Sauria MEG, Sanyal A, Gerasimova TI, Lajoie BR, Bell JSK, Ong C-T, Hookway TA, Guo C, Sun Y, et al. 2013. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153: 1281-1295.
49. Pryde FE, Louis EJ. 1999. Limitations of silencing at native yeast telomeres. EMBO J 18: 2538-2550.
50. Radman-Livaja M, Ruben G, Weiner A, Friedman N, Kamakaka R, Rando OJ. 2011. Dynamics of Sir3 spreading in budding yeast: Secondary recruitment sites and euchromatic localization. EMBO J 30: 1012-1026.
51. Ravindra A, Weiss K, Simpson RT. 1999. High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating-type locus HMRa. Mol Cell Biol 19: 7944-7950.
52. Rine J, Strathern JN, Hicks JB, Herskowitz I. 1979. A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: Evidence for and identification of cryptic mating-type loci. Genetics 93: 877-901.
53. Ringrose L, Paro R. 2004. Epigenetic regulation of cellular memory by the polycomb and trithorax group proteins. Annu Rev Genet 38: 413-443.
54. Rivier DH, Ekena JL, Rine J. 1999. HMR-I is an origin of replication and a silencer in Saccharomyces cerevisiae. Genetics 151: 521-529.
55. Rusche LN, Kirchmaier AL, Rine J. 2002. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol Biol Cell 13: 2207-2222.
56. Rusche LN, Kirchmaier AL, Rine J. 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72: 481-516.
57. Singh J, Klar AJ. 1992. Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: A novel in vivo probe for chromatin structure of yeast. Genes Dev 6: 186-196.
58. +-dependent protein deacetylase activity in the Sir2 protein family. Proc Natl Acad Sci 97: 6658-6663.
59. Sperling AS, Grunstein M. 2009. Histone H3 N-terminus regulates higher order structure of yeast heterochromatin. Proc Natl Acad Sci 106: 13153-13159.
60. Strathern JN, Klar AJ, Hicks JB, Abraham JA, Ivy JM, Nasmyth KA, McGill C. 1982. Homothallic switching of yeast mating type cassettes is initiated by a double-stranded cut in the MAT locus. Cell 31: 183-192.
61. Suka N, Suka Y, Carmen AA, Wu J, Grunstein M. 2001. Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol Cell 8: 473-479.
62. Suka N, Luo K, Grunstein M. 2002. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat Genet 32: 378-383.
63. Takahashi Y-H, Schulze JM, Jackson J, Hentrich T, Seidel C, Jaspersen SL, Kobor MS, Shilatifard A. 2011. Dot1 and histone H3K79 methylation in natural telomeric and HM silencing. Mol Cell 42: 118-126.
64. Tanny JC, Dowd GJ, Huang J, Hilz H, Moazed D. 1999. An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99: 735-745.
65. Teytelman L, Özaydi{dotless}n B, Zill O, Lefrancxois P, Snyder M, Rine J, Eisen MB. 2009. Impact of chromatin structures on DNA processing for genomic analyses. PLoS ONE 4: e6700.
66. Teytelman L, Thurtle DM, Rine J, van Oudenaarden A. 2013. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci 110: 18602-18607.
67. Triolo T, Sternglanz R. 1996. Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. Nature 381: 251-253.
68. Valenzuela L, Dhillon N, Dubey RN, Gartenberg MR, Kamakaka RT. 2008. Long-range communication between the silencers of HMR. Mol Cell Biol 28: 1924-1935.
69. Wang F, Li G, Altaf M, Lu C, Currie MA, Johnson A, Moazed D. 2013. Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA. Proc Natl Acad Sci 110: 8495-8500.
70. Weiss K, Simpson RT. 1998. High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLa. Mol Cell Biol 18: 5392-5403.
71. Wu C-S, Chen Y-F, Gartenberg MR. 2011. Targeted sister chromatid cohesion by Sir2. PLoS Genet 7: e1002000.
72. Yu Q, Olsen L, Zhang X, Boeke JD, Bi X. 2011. Differential contributions of histone H3 and H4 residues to heterochromatin structure. Genetics 188: 291-308.
73. Zhang Z, Hayashi MK, Merkel O, Stillman B, Xu R-M. 2002. Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing. EMBO J 21: 4600-4611.
74. Zhu X, Gustafsson CM. 2009. Distinct differences in chromatin structure at subtelomeric X and Y9 elements in budding yeast. PLoS ONE 4: e6363.
75. Zill OA, Scannell D, Teytelman L, Rine J. 2010. Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol 8: e1000550.