Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae

Molecular and Cellular Biology

Volumn 25, Issue 22, 2005, Pages 10060-10070

  Hyland, Edel M ^a   Cosgrove, Michael S ^a,c   Molina, Henrik ^a   Wang, Dongxia ^a,d   Pandey, Akhilesh ^a   Cottee, Robert J ^a   Boeke, Jef D ^a,b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b 339 Broadway Research Building ^*  (United States)

^c SYRACUSE UNIVERSITY   (United States)

^d NATL CENTER FOR INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; HISTONE H4;

ACETYLATION; ALLELE; ARTICLE; DNA DAMAGE; DNA METABOLISM; DNA MODIFICATION; DNA REPAIR; GENE LOCUS; GENE MUTATION; GENE SILENCING; GENETIC CONSERVATION; GENETIC VARIABILITY; HETEROCHROMATIN; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; RESIDUE ANALYSIS; SACCHAROMYCES CEREVISIAE; TELOMERE;

ALLELES; AMINO ACID SEQUENCE; BLOTTING, SOUTHERN; DNA; DNA DAMAGE; DNA REPAIR; EVOLUTION, MOLECULAR; GENE SILENCING; HETEROCHROMATIN; HISTONES; MASS SPECTROMETRY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; MUTATION; NUCLEOSOMES; PHENOTYPE; PLASMIDS; PROTEIN PROCESSING, POST-TRANSLATIONAL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRANSCRIPTION, GENETIC;

BOVINAE; SACCHAROMYCES CEREVISIAE;

EID: 27644467857     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.22.10060-10070.2005     Document Type: Article

References (54)

1. Becker, P. B., and W. Horz. 2002. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71:247-273.
2. Chang, C. H., and D. S. Luse. 1997. The H3/H4 tetramer blocks transcript elongation by RNA polymerase II in vitro. J. Biol. Chem. 272:23427-23434.
3. Cheung, W. L., F. B. Turner, T. Krishnamoorthy, B. Wolner, S. H. Ahn, M. Foley, J. A. Dorsey, C. L. Peterson, S. L. Berger, and C. D. Allis. 2005. Phosphorylation of histone H4 serine 1 during DNA damage requires casein kinase II in S. cerevisiae. Curr. Biol. 15:656-660.
4. Cosgrove, M. S., J. D. Boeke, and C. Wolberger. 2004. Regulated nucleosome mobility and the histone code. Nat. Struct. Mol. Biol. 11:1037-1043.
5. Cost, G. J., and J. D. Boeke. 1996. A useful colony colour phenotype associated with the yeast selectable/counter-selectable marker MET15. Yeast 12:939-941.
6. Davey, C. A., D. F. Sargent, K. Luger, A. W. Maeder, and T. J. Richmond. 2002. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319:1097-1113.
7. de la Cruz, X., S. Lois, S. Sanchez-Molina, and M. A. Martinez-Balbas. 2005. Do protein motifs read the histone code? Bioessays 27:164-175.
8. Delano, W. L. 2002. The PyMOL molecular graphics system. Delano Scientific, San Carlos, Calif.
9. De Rubertis, F., D. Kadosh, S. Henchoz, D. Pauli, G. Reuter, K. Strahl, and P. Spierer. 1996. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature 384:589-591.
10. Dion, M. F., S. J. Altschuler, L. F. Wu, and O. J. Rando. 2005. From the cover: genomic characterization reveals a simple histone H4 acetylation code. Proc. Natl. Acad. Sci. USA 102:5501-5506.
11. Dorigo, B., T. Schalch, K. Bystricky, and T. J. Richmond. 2003. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J. Mol. Biol. 327:85-96.
12. Duina, A. A., and F. Winston. 2004. Analysis of a mutant histone H3 that perturbs the association of Swi/Snf with chromatin. Mol. Cell. Biol. 24: 561-572.
13. Eissenberg, J. C. 2001. Molecular biology of the chromo domain: an ancient chromatin module comes of age. Gene 275:19-29.
14. Feng, Q., H. Wang, H. H. Ng, H. Erdjument-Bromage, P. Tempst, K. Struhl, and Y. Zhang. 2002. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12:1052-1058.
15. Fritze, C. E., K. Verschueren, R. Strich, and R. Easton Esposito. 1997. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J. 16:6495-6509.
16. Glowczewski, L., P. Yang, T. Kalashnikova, M. S. Santisteban, and M. M. Smith. 2000. Histone-histone interactions and centromere function. Mol. Cell. Biol. 20:5700-5711.
17. Hassan, A. H., P. Prochasson, K. E. Neely, S. C. Galasinski, M. Chandy, M. J. Carrozza, and J. L. Workman. 2002. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111:369-379.
18. Hirschhorn, J. N., A. L. Bortvin, S. L. Ricupero-Hovasse, and F. Winston. 1995. A new class of histone H2A mutations in Saccharomyces cerevisiae causes specific transcriptional defects in vivo. Mol. Cell. Biol. 15:1999-2009.
19. Iizuka, M., and M. M. Smith. 2003. Functional consequences of histone modifications. Curr. Opin. Genet. Dev. 13:154-160.
20. Jenuwein, T., and C. D. Allis. 2001. Translating the histone code. Science 293:1074-1080.
21. Johnson, L. M., P. S. Kayne, E. S. Kahn, and M. Grunstein. 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. USA 87:6286-6290.
22. Jones, D. O., I. G. Cowell, and P. B. Singh. 2000. Mammalian chromodomain proteins: their role in genome organisation and expression. Bioessays 22: 124-137.
23. Kasten, M., H. Szerlong, H. Erdjument-Bromage, P. Tempst, M. Werner, and B. R. Cairns. 2004. Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. EMBO J. 23:1348-1359.
24. Kayne, P. S., U. J. Kim, M. Han, J. R. Mullen, F. Yoshizaki, and M. Grunstein. 1988. Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell 55:27-39.
25. Kouzarides, T. 2002. Histone methylation in transcriptional control. Curr. Opin. Genet. Dev. 12:198-209.
26. Kruger, W., C. L. Peterson, A. Sil, C. Coburn, G. Arents, E. N. Moudrianakis, and I. Herskowitz. 1995. Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev. 9:2770-2779.
27. Lacoste, N., R. T. Utley, J. M. Hunter, G. G. Poirier, and J. Cote. 2002. Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J. Biol. Chem. 277:30421-30424.
28. Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent, and T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251-260.
29. Lusser, A., D. L. Urwin, and J. T. Kadonaga. 2005. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat. Struct. Mol. Biol. 12:160-166.
30. Masumoto, H., D. Hawke, R. Kobayashi, and A. Verreault. 2005. A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature 436:294-298.
31. Megee, P. C., B. A. Morgan, B. A. Mittman, and M. M. Smith. 1990. Genetic analysis of histone H4: essential role of lysines subject to reversible acetylation. Science 247:841-845.
32. Megee, P. C., B. A. Morgan, and M. M. Smith. 1995. Histone H4 and the maintenance of genome integrity. Genes Dev. 9:1716-1727.
33. Moore, J. D., and J. E. Krebs. 2004. Histone modifications and DNA double-strand break repair. Biochem. Cell Biol. 82:446-452.
34. Muthurajan, U. M., Y. Bao, L. J. Forsberg, R. S. Edayathumangalam, P. N. Dyer, C. L. White, and K. Luger. 2004. Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J. 23:260-271.
35. Narlikar, G. J., H. Y. Fan, and R. E. Kingston. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108: 475-487.
36. Ng, H. H., R. M. Xu, Y. Zhang, and K. Struhl. 2002. Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J. Biol. Chem. 277:34655-34657.
37. +, a putative fission yeast histone deacetylase gene. Nucleic Acids Res. 26:3247-3254.
38. Park, J. H., M. S. Cosgrove, E. Youngman, C. Wolberger, and J. D. Boeke. 2002. A core nucleosome surface crucial for transcriptional silencing. Nat. Genet. 32:273-279.
39. Prelich, G., and F. Winston. 1993. Mutations that suppress the deletion of an upstream activating sequence in yeast: involvement of a protein kinase and histone H3 in repressing transcription in vivo. Genetics 135:665-676.
40. Recht, J., and M. A. Osley. 1999. Mutations in both the structured domain and N-terminus of histone H2B bypass the requirement for Swi-Snf in yeast. EMBO J. 18:229-240.
41. Roth, S. Y., J. M. Denu, and C. D. Allis. 2001. Histone acetyltransferases. Annu. Rev. Biochem. 70:81-120.
42. Sanders, S. L., M. Portoso, J. Mata, J. Bahler, R. C. Allshire, and T. Kouzarides. 2004. Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell 119:603-614.
43. Sikorski, R. S., 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.
44. Singer, M. S., and D. E. Gottschling. 1994. TLC1: template RNA component of Saccharomyces cerevisiae telomerase. Science 266:404-409.
45. Smith, J. S., and J. D. Boeke. 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11:241-254.
46. Smith, J. S., E. Caputo, and J. D. Boeke. 1999. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol. Cell. Biol. 19:3184-3197.
47. Smith, M. M., and M. S. Santisteban. 1998. Genetic dissection of histone function. Methods 15:269-281.
48. Strahl, B. D., and C. D. Allis. 2000. The language of covalent histone modifications. Nature 403:41-45.
49. van Leeuwen, F., P. R. Gafken, and D. E. Gottschling. 2002. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109: 745-756.
50. White, C. L., R. K. Suto, and K. Luger. 2001. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J. 20:5207-5218.
51. Xu, F., K. Zhang, and M. Grunstein. 2005. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell 121:375-385.
52. Ye, J., X. Ai, E. E. Eugeni, L. Zhang, L. R. Carpenter, M. A. Jelinek, M. A. Freitas, and M. R. Parthun. 2005. Histone H4 lysine 91 acetylation A core domain modification associated with chromatin assembly. Mol. Cell 18: 123-130.
53. Zhang, K., P. M. Yau, B. Chandrasekhar, R. New, R. Kondrat, B. S. Imai, and M. E. Bradbury. 2004. Differentiation between peptides containing acetylated or tri-methylated lysines by mass spectrometry: an application for determining lysine 9 acetylation and methylation of histone H3. Proteomics 4:1-10.
54. Zhang, L., E. E. Eugeni, M. R. Parthun, and M. A. Freitas. 2003. Identification of novel histone posttranslational modifications by peptide mass fingerprinting. Chromosoma 112:77-86.