Genome-wide patterns of histone modifications in yeast (original) (raw)
Grunstein, M. Histone function in transcription. Annu. Rev. Cell Biol.6, 643–678 (1990). CASPubMed Google Scholar
Cheung, W. L., Briggs, S. D. & Allis, C. D. Acetylation and chromosomal functions. Curr. Opin. Cell Biol.12, 326–333 (2000). CASPubMed Google Scholar
Martin, C. & Zhang, Y. The diverse functions of histone lysine methylation. Nature Rev. Mol. Cell Biol.6, 838–849 (2005). CAS Google Scholar
Johnson, L. M., Kayne, P. S., Kahn, E. S. & Grunstein, M. 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. USA87, 6286–6290 (1990). CASPubMed Google Scholar
Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature406, 593–599 (2000). CASPubMed Google Scholar
Braunstein, M., Rose, A. B., Holmes, S. G., Allis, C. D. & Broach, J. R. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev.7, 592–604 (1993). CASPubMed Google Scholar
Vogelauer, M., Rubbi, L., Lucas, I., Brewer, B. J. & Grunstein, M. Histone acetylation regulates the time of replication origin firing. Mol. Cell10, 1223–1233 (2002). CASPubMed Google Scholar
Ahn, S. H. et al. Sterile 20 kinase phosphorylates histone H2B at serine 10 during hydrogen peroxide-induced apoptosis in S. cerevisiae. Cell120, 25–36 (2005). CASPubMed Google Scholar
van Attikum, H. & Gasser, S. M. The histone code at DNA breaks: a guide to repair? Nature Rev. Mol. Cell Biol.6, 757–765 (2005). CAS Google Scholar
Kurdistani, S. K., Tavazoie, S. & Grunstein, M. Mapping global histone acetylation patterns to gene expression. Cell117, 721–733 (2004). Genome-wide comparison of many histone acetylation sites inS. cerevisiae, which shows that sites are acetylated differentially, generating patterns that correlate with gene activity. CASPubMed Google Scholar
Smith, C. M. et al. Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4. Anal. Biochem.316, 23–33 (2003). CASPubMed Google Scholar
Boyne, M. T. 2nd, Pesavento, J. J., Mizzen, C. A. & Kelleher, N. L. Precise characterization of human histones in the H2A gene family by top down mass spectrometry. J. Proteome Res.5, 248–253 (2006). CASPubMed Google Scholar
Thomas, C. E., Kelleher, N. L. & Mizzen, C. A. Mass spectrometric characterization of human histone H3: a bird's eye view. J. Proteome Res.5, 240–247 (2006). CASPubMed Google Scholar
Clarke, D. J., O'Neill, L. P. & Turner, B. M. Selective use of H4 acetylation sites in the yeast Saccharomyces cerevisiae. Biochem. J.294, 557–561 (1993). CASPubMedPubMed Central Google Scholar
Turner, B. M., O'Neill, L. P. & Allan, I. M. Histone H4 acetylation in human cells. Frequency of acetylation at different sites defined by immunolabeling with site-specific antibodies. FEBS Lett.253, 141–145 (1989). CASPubMed Google Scholar
Suka, N., Suka, Y., Carmen, A. A., Wu, J. & Grunstein, M. Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol. Cell8, 473–479 (2001). CASPubMed Google Scholar
Sarma, K., Nishioka, K. & Reinberg, D. Tips in analyzing antibodies directed against specific histone tail modifications. Methods Enzymol.376, 255–269 (2004). CASPubMed Google Scholar
Kurdistani, S. K. & Grunstein, M. In vivo protein–protein and protein–DNA crosslinking for genomewide binding microarray. Methods31, 90–95 (2003). CASPubMed Google Scholar
Robyr, D. & Grunstein, M. Genomewide histone acetylation microarrays. Methods31, 83–89 (2003). CASPubMed Google Scholar
Rao, B., Shibata, Y., Strahl, B. D. & Lieb, J. D. Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol. Cell. Biol.25, 9447–9459 (2005). Genome-wide study of H3K36 methylation, which shows that this modification is restricted to the coding regions of active genes. CASPubMedPubMed Central Google Scholar
Liu, C. L. et al. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol.3, e328 (2005). Describes the mapping of histone modifications at single-nucleosome resolution onS. cerevisiaechromosome III, and shows that the modification pattern of nucleosomes surrounding the transcription start site differs from that of coding-region nucleosomes. PubMedPubMed Central Google Scholar
Pokholok, D. K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell122, 517–527 (2005). High-resolution, genome-wide analysis ofS. cerevisiaechromosomes, which shows that acetylation at sites in H3 correlates with transcription. CASPubMed Google Scholar
Xu, F., Zhang, K. & Grunstein, M. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell121, 375–385 (2005). CASPubMed Google Scholar
Millar, C. B., Xu, F., Zhang, K. & Grunstein, M. Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast. Genes Dev.20, 711–722 (2006). CASPubMedPubMed Central Google Scholar
Wiren, M. et al. Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J.24, 2906–2918 (2005). CASPubMedPubMed Central Google Scholar
Cam, H. P. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nature Genet.37, 809–819 (2005). CASPubMed Google Scholar
Schubeler, D. et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev.18, 1263–1271 (2004). PubMedPubMed Central Google Scholar
Mito, Y., Henikoff, J. G. & Henikoff, S. Genome-scale profiling of histone H3.3 replacement patterns. Nature Genet.37, 1090–1097 (2005). CASPubMed Google Scholar
Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell120, 169–181 (2005). CASPubMed Google Scholar
Nishida, H. et al. Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell. Chromosome Res.14, 203–211 (2006). CASPubMed Google Scholar
Tse, C., Sera, T., Wolffe, A. P. & Hansen, J. C. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol. Cell. Biol.18, 4629–4638 (1998). CASPubMedPubMed Central Google Scholar
Zheng, C. & Hayes, J. J. Intra- and inter-nucleosomal protein–DNA interactions of the core histone tail domains in a model system. J. Biol. Chem.278, 24217–24224 (2003). CASPubMed Google Scholar
Dorigo, B., Schalch, T., Bystricky, K. & Richmond, T. J. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J. Mol. Biol.327, 85–96 (2003). CASPubMed Google Scholar
Shogren-Knaak, M. et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science311, 844–847 (2006). Shows that acetylation of a single site (K16) in H4 regulates higher orders of folding of nucleosome arraysin vitro. CASPubMed Google Scholar
Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature410, 116–120 (2001). Identifies the chromodomain as a methyl-lysine-binding module. CASPubMed Google Scholar
Huyen, Y. et al. Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature432, 406–411 (2004). CASPubMed Google Scholar
Wysocka, J. et al. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell121, 859–872 (2005). CASPubMed Google Scholar
Dhalluin, C. et al. Structure and ligand of a histone acetyltransferase bromodomain. Nature399, 491–496 (1999). Identifies the bromodomain as an acetyl-lysine-recognition domain. CASPubMed Google Scholar
Jacobson, R. H., Ladurner, A. G., King, D. S. & Tjian, R. Structure and function of a human TAFII250 double bromodomain module. Science288, 1422–1425 (2000). CASPubMed Google Scholar
Zeng, L. & Zhou, M. M. Bromodomain: an acetyl-lysine binding domain. FEBS Lett.513, 124–128 (2002). CASPubMed Google Scholar
Carmen, A. A., Milne, L. & Grunstein, M. Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. J. Biol. Chem.277, 4778–4781 (2002). CASPubMed Google Scholar
Liou, G. G., Tanny, J. C., Kruger, R. G., Walz, T. & Moazed, D. Assembly of the SIR complex and its regulation by _O_-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell121, 515–527 (2005). Shows that acetylation of H4K16 disrupts interaction between full-length Sir3 and a peptide that corresponds to the N terminus of H4. CASPubMed Google Scholar
Rayasam, G. V. et al. NSD1 is essential for early post-implantation development and has a catalytically active SET domain. EMBO J.22, 3153–163 (2003). CASPubMedPubMed Central Google Scholar
Wang, A., Kurdistani, S. K. & Grunstein, M. Requirement of Hos2 histone deacetylase for gene activity in yeast. Science298, 1412–1414 (2002). CASPubMed Google Scholar
Imai, S. et al. Sir2: an NAD-dependent histone deacetylase that connects chromatin silencing, metabolism, and aging. Cold Spring Harb. Symp. Quant. Biol.65, 297–302 (2000). CASPubMed Google Scholar
Landry, J. et al. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc. Natl Acad. Sci. USA97, 5807–5811 (2000). CASPubMed Google Scholar
Sutton, A. et al. Sas4 and Sas5 are required for the histone acetyltransferase activity of Sas2 in the SAS complex. J. Biol. Chem.278, 16887–16892 (2003). CASPubMed Google Scholar
Kimura, A., Umehara, T. & Horikoshi, M. Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nature Genet.32, 370–377 (2002). PubMed Google Scholar
Suka, N., Luo, K. & Grunstein, M. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nature Genet.32, 378–383 (2002). CASPubMed Google Scholar
Reid, J. L., Iyer, V. R., Brown, P. O. & Struhl, K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol. Cell6, 1297–1307 (2000). CASPubMed Google Scholar
Kadosh, D. & Struhl, K. Targeted recruitment of the Sin3–Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell. Biol.18, 5121–5127 (1998). CASPubMedPubMed Central Google Scholar
Kurdistani, S. K., Robyr, D., Tavazoie, S. & Grunstein, M. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nature Genet.31, 248–254 (2002). CASPubMed Google Scholar
Robert, F. et al. Global position and recruitment of HATs and HDACs in the yeast genome. Mol. Cell16, 199–209 (2004). CASPubMedPubMed Central Google Scholar
Vogelauer, M., Wu, J., Suka, N. & Grunstein, M. Global histone acetylation and deacetylation in yeast. Nature408, 495–498 (2000). CASPubMed Google Scholar
Boudreault, A. A. et al. Yeast enhancer of polycomb defines global Esa1-dependent acetylation of chromatin. Genes Dev.17, 1415–1428 (2003). CASPubMedPubMed Central Google Scholar
Waterborg, J. H. Steady-state levels of histone acetylation in Saccharomyces cerevisiae. J. Biol. Chem.275, 13007–13011 (2000). CASPubMed Google Scholar
Grunstein, M. Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell93, 325–328 (1998). CASPubMed Google Scholar
Ng, H. H., Robert, F., Young, R. A. & Struhl, K. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell11, 709–719 (2003). CASPubMed Google Scholar
Xiao, T. et al. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev.17, 654–663 (2003). CASPubMedPubMed Central Google Scholar
Keogh, M. C. et al. Cotranscriptional Set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell123, 593–605 (2005). CASPubMed Google Scholar
Joshi, A. A. & Struhl, K. Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol. Cell20, 971–978 (2005). CASPubMed Google Scholar
Carrozza, M. J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell123, 581–592 (2005). CASPubMed Google Scholar
Shahbazian, M. D., Zhang, K. & Grunstein, M. Histone H2B ubiquitylation controls processive methylation but not monomethylation by Dot1 and Set1. Mol. Cell19, 271–277 (2005). CASPubMed Google Scholar
Cubizolles, F., Martino, F., Perrod, S. & Gasser, S. M. A homotrimer–heterotrimer switch in Sir2 structure differentiates rDNA and telomeric silencing. Mol. Cell21, 825–836 (2006). CASPubMed Google Scholar
Robyr, D. et al. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell109, 437–446 (2002). First genome-wide analysis of histone modifications, which identifies unique chromosomal domains that are affected by specific histone deacetylases inS. cerevisiae. CASPubMed Google Scholar
Katan-Khaykovich, Y. & Struhl, K. Heterochromatin formation involves changes in histone modifications over multiple cell generations. EMBO J.24, 2138–2149 (2005). CASPubMedPubMed Central Google Scholar
Hecht, A., Laroche, T., Strahl-Bolsinger, S., Gasser, S. M. & Grunstein, M. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell80, 583–592 (1995). CASPubMed Google Scholar
Donze, D., Adams, C. R., Rine, J. & Kamakaka, R. T. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev.13, 698–708 (1999). CASPubMedPubMed Central Google Scholar
Thompson, J. S., Ling, X. & Grunstein, M. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature369, 245–247 (1994). CASPubMed Google Scholar
Sullivan, B. A. & Karpen, G. H. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nature Struct. Mol. Biol.11, 1076–1083 (2004). CAS Google Scholar
Blower, M. D., Sullivan, B. A. & Karpen, G. H. Conserved organization of centromeric chromatin in flies and humans. Dev. Cell2, 319–330 (2002). CASPubMedPubMed Central Google Scholar
Meluh, P. B., Yang, P., Glowczewski, L., Koshland, D. & Smith, M. M. Cse4p is a component of the core centromere of Saccharomyces cerevisiae. Cell94, 607–613 (1998). CAS Google Scholar
Riedel, C. G. et al. Protein phosphatase 2A protects centromeric sister chromatid cohesion during meiosis I. Nature441, 53–61 (2006). CASPubMed Google Scholar
Masumoto, H., Hawke, D., Kobayashi, R. & Verreault, A. A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature436, 294–298 (2005). CASPubMed Google Scholar
Wu, J., Suka, N., Carlson, M. & Grunstein, M. TUP1 utilizes histone H3/H2B-specific HDA1 deacetylase to repress gene activity in yeast. Mol. Cell7, 117–126 (2001). CASPubMed Google Scholar
Meneghini, M. D., Wu, M. & Madhani, H. D. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell112, 725–36 (2003). Identification of groups of subtelomeric genes, the expression of which is regulated by the histone variant H2A.Z. CASPubMed Google Scholar
Raisner, R. M. et al. Histone variant H2A. Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell123, 233–248 (2005). CASPubMedPubMed Central Google Scholar
Zhang, H., Roberts, D. N. & Cairns, B. R. Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell123, 219–231 (2005). CASPubMedPubMed Central Google Scholar
Guillemette, B. et al. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol.3, e384 (2005). PubMedPubMed Central Google Scholar
Li, B. et al. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc. Natl Acad. Sci. USA102, 18385–18390 (2005). CASPubMed Google Scholar
Aparicio, J. G., Viggiani, C. J., Gibson, D. G. & Aparicio, O. M. The Rpd3–Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol. Cell. Biol.24, 4769–4780 (2004). CASPubMedPubMed Central Google Scholar
Boeger, H., Griesenbeck, J., Strattan, J. S. & Kornberg, R. D. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol. Cell14, 667–673 (2004). CASPubMed Google Scholar
Reinke, H. & Horz, W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell11, 1599–1607 (2003). CASPubMed Google Scholar
Adkins, M. W., Howar, S. R. & Tyler, J. K. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol. Cell14, 657–666 (2004). CASPubMed Google Scholar
Korber, P. et al. The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters. J. Biol. Chem.281, 5539–5545 (2006). CASPubMed Google Scholar
Lee, C. K., Shibata, Y., Rao, B., Strahl, B. D. & Lieb, J. D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nature Genet.36, 900–905 (2004). CASPubMed Google Scholar
Bernstein, B. E., Liu, C. L., Humphrey, E. L., Perlstein, E. O. & Schreiber, S. L. Global nucleosome occupancy in yeast. Genome Biol.5, R62 (2004). PubMedPubMed Central Google Scholar
Struhl, K., Kadosh, D., Keaveney, M., Kuras, L. & Moqtaderi, Z. Activation and repression mechanisms in yeast. Cold Spring Harb. Symp. Quant. Biol.63, 413–421 (1998). CASPubMed Google Scholar
Krebs, J. E., Kuo, M. H., Allis, C. D. & Peterson, C. L. Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. Genes Dev.13, 1412–1421 (1999). CASPubMedPubMed Central Google Scholar
Kuo, M. H., vom Baur, E., Struhl, K. & Allis, C. D. Gcn4 activator targets Gcn5 histone acetyltransferase to specific promoters independently of transcription. Mol. Cell6, 1309–1320 (2000). CASPubMed Google Scholar
Zhao, J., Herrera-Diaz, J. & Gross, D. S. Domain-wide displacement of histones by activated heat shock factor occurs independently of Swi/Snf and is not correlated with RNA polymerase II density. Mol. Cell. Biol.25, 8985–8999 (2005). CASPubMedPubMed Central Google Scholar
Guo, X., Tatsuoka, K. & Liu, R. Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. Bioinformatics22, 392–399 (2006). CASPubMed Google Scholar
Matangkasombut, O., Buratowski, R. M., Swilling, N. W. & Buratowski, S. Bromodomain factor 1 corresponds to a missing piece of yeast TFIID. Genes Dev.14, 951–962 (2000). CASPubMedPubMed Central Google Scholar
Eisen, A. et al. The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J. Biol. Chem.276, 3484–3491 (2001). CASPubMed Google Scholar
Hassan, A. H. et al. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell111, 369–379 (2002). CASPubMed Google Scholar
Kasten, M. et al. Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. EMBO J.23, 1348–1359 (2004). CASPubMedPubMed Central Google Scholar
Ladurner, A. G., Inouye, C., Jain, R. & Tjian, R. Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol. Cell11, 365–376 (2003). CASPubMed Google Scholar
Matangkasombut, O. & Buratowski, S. Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. Mol. Cell11, 353–363 (2003). CASPubMed Google Scholar
Shankaranarayana, G. D., Motamedi, M. R., Moazed, D. & Grewal, S. I. Sir2 regulates histone H3 lysine 9 methylation and heterochromatin assembly in fission yeast. Curr. Biol.13, 1240–1246 (2003). CASPubMed Google Scholar
Wirbelauer, C., Bell, O. & Schubeler, D. Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias. Genes Dev.19, 1761–1766 (2005). CASPubMedPubMed Central Google Scholar
Sinha, I., Wiren, M. & Ekwall, K. Genome-wide patterns of histone modifications in fission yeast. Chromosome Res.14, 95–105 (2006). CASPubMed Google Scholar
Ahmad, K. & Henikoff, S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell9, 1191–1200 (2002). CASPubMed Google Scholar
De Nadal, E. et al. The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature427, 370–374 (2004). CASPubMed Google Scholar
Grant, P. A., et al. Expanded lysine acetylation specificity of Gcn5 in native complexes. J. Biol Chem.274, 5895–5900 (1999). CASPubMed Google Scholar
Maas, N. L., Miller, K. M., DeFazio, L. G. & Toczyski, D. P. Cell cycle and checkpoint regulation of histone H3K56 acetylation by Hst3 and Hst4. Mol. Cell23, 109–119 (2006). CASPubMed Google Scholar
Celic, I. et al. The sirtuins Hst3 and Hst4p preserve genome integrity by controlling histone H3 lysine 56 deacetylation. Curr. Biol.16, 1280–1289 (2006). CASPubMed Google Scholar