Insights into the Role of Histone H3 and Histone H4 Core Modifiable Residues in Saccharomyces cerevisiae

REFERENCES

• Becker, P. B., and W. Horz. 2002. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71:247–273.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Cosgrove, M. S., J. D. Boeke, and C. Wolberger. 2004. Regulated nucleosome mobility and the histone code. Nat. Struct. Mol. Biol. 11:1037–1043.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Delano, W. L. 2002. The PyMOL molecular graphics system. Delano Scientific, San Carlos, Calif.
   Google Scholar
• De Rubertis, F., D. Kadosh, S. Henchoz, D. Pauli, G. Reuter, K. Struhl, and P. Spierer. 1996. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature 384:589–591.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Eissenberg, J. C. 2001. Molecular biology of the chromo domain: an ancient chromatin module comes of age. Gene 275:19–29.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Iizuka, M., and M. M. Smith. 2003. Functional consequences of histone modifications. Curr. Opin. Genet. Dev. 13:154–160.
   PubMed Web of Science ®Google Scholar
• Jenuwein, T., and C. D. Allis. 2001. Translating the histone code. Science 293:1074–1080.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Kouzarides, T. 2002. Histone methylation in transcriptional control. Curr. Opin. Genet. Dev. 12:198–209.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Megee, P. C., B. A. Morgan, and M. M. Smith. 1995. Histone H4 and the maintenance of genome integrity. Genes Dev. 9:1716–1727.
   PubMed Web of Science ®Google Scholar
• Moore, J. D., and J. E. Krebs. 2004. Histone modifications and DNA double-strand break repair. Biochem. Cell Biol. 82:446–452.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Narlikar, G. J., H. Y. Fan, and R. E. Kingston. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475–487.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Olsson, T. G., K. Ekwall, R. C. Allshire, P. Sunnerhagen, J. F. Partridge, and W. A. Richardson. 1998. Genetic characterisation of hda1+, a putative fission yeast histone deacetylase gene. Nucleic Acids Res. 26:3247–3254.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Roth, S. Y., J. M. Denu, and C. D. Allis. 2001. Histone acetyltransferases. Annu. Rev. Biochem. 70:81–120.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Singer, M. S., and D. E. Gottschling. 1994. TLC1: template RNA component of Saccharomyces cerevisiae telomerase. Science 266:404–409.
   PubMed Web of Science ®Google Scholar
• Smith, J. S., and J. D. Boeke. 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11:241–254.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Smith, M. M., and M. S. Santisteban. 1998. Genetic dissection of histone function. Methods 15:269–281.
   PubMedGoogle Scholar
• Strahl, B. D., and C. D. Allis. 2000. The language of covalent histone modifications. Nature 403:41–45.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Xu, F., K. Zhang, and M. Grunstein. 2005. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell 121:375–385.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar