Genome-wide patterns of histone modifications in yeast

Post-translational histone modifications and histone variants generate complexity in chromatin to enable the many functions of the chromosome. Recent studies have mapped histone modifications across the Saccharomyces cerevisiae genome. These experiments describe how combinations of modified and unmodified states relate to each other and particularly to chromosomal landmarks that include heterochromatin, subtelomeric chromatin, centromeres, origins of replication, promoters and coding regions. Such patterns might be important for the regulation of heterochromatin-mediated silencing, chromosome segregation, DNA replication and gene expression.

[1]  J Wu,et al.  Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. , 2001, Molecular cell.

[2]  Kevin Struhl,et al.  Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. , 2005, Molecular cell.

[3]  Hiten D. Madhani,et al.  Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin , 2003, Cell.

[4]  M. Grunstein.  Histone function in transcription. , 1990, Annual review of cell biology.

[5]  Christoph H Borchers,et al.  Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. , 2003, Genes & development.

[6]  T. Richmond,et al.  Chromatin fiber folding: requirement for the histone H4 N-terminal tail. , 2003, Journal of molecular biology.

[7]  N. Friedman,et al.  Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae , 2005, PLoS biology.

[8]  William Arbuthnot Sir Lane,et al.  The Yeast NuA4 and Drosophila MSL Complexes Contain Homologous Subunits Important for Transcription Regulation* , 2001, The Journal of Biological Chemistry.

[9]  C. Allis,et al.  Acetylation and chromosomal functions. , 2000, Current Opinion in Cell Biology.

[10]  Michael Grunstein,et al.  Global histone acetylation and deacetylation in yeast , 2000, Nature.

[11]  Michael Grunstein,et al.  Histone acetylation regulates the time of replication origin firing. , 2002, Molecular cell.

[12]  R. Tjian,et al.  Structure and function of a human TAFII250 double bromodomain module. , 2000, Science.

[13]  J. Rine,et al.  The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. , 1999, Genes & development.

[14]  S. Henikoff,et al.  Genome-scale profiling of histone H3.3 replacement patterns , 2005, Nature Genetics.

[15]  Karl Mechtler,et al.  Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins , 2001, Nature.

[16]  C. Allis,et al.  Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. , 1999, Genes & development.

[17]  J Seth Strattan,et al.  Removal of promoter nucleosomes by disassembly rather than sliding in vivo. , 2004, Molecular cell.

[18]  Lei Zeng,et al.  Structure and ligand of a histone acetyltransferase bromodomain , 1999, Nature.

[19]  J. Workman,et al.  Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[20]  K. Struhl,et al.  Targeted Recruitment of the Sin3-Rpd3 Histone Deacetylase Complex Generates a Highly Localized Domain of Repressed Chromatin In Vivo , 1998, Molecular and Cellular Biology.

[21]  K. Struhl,et al.  Gcn4 activator targets Gcn5 histone acetyltransferase to specific promoters independently of transcription. , 2000, Molecular cell.

[22]  Thomas Walz,et al.  Assembly of the SIR Complex and Its Regulation by O-Acetyl-ADP-Ribose, a Product of NAD-Dependent Histone Deacetylation , 2005, Cell.

[23]  M. Grunstein,et al.  Acetylation in Histone H3 Globular Domain Regulates Gene Expression in Yeast , 2005, Cell.

[24]  Gary H Karpen,et al.  Conserved organization of centromeric chromatin in flies and humans. , 2002, Developmental cell.

[25]  Tom J. Petty,et al.  Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks , 2004, Nature.

[26]  Sung-Hee Ahn,et al.  Sterile 20 Kinase Phosphorylates Histone H2B at Serine 10 during Hydrogen Peroxide-Induced Apoptosis in S. cerevisiae , 2005, Cell.

[27]  J. H. Waterborg,et al.  Steady-state Levels of Histone Acetylation in Saccharomyces cerevisiae * , 2000, The Journal of Biological Chemistry.

[28]  David A. Band,et al.  Sas4 and Sas5 Are Required for the Histone Acetyltransferase Activity of Sas2 in the SAS Complex* , 2003, The Journal of Biological Chemistry.

[29]  Michael Grunstein,et al.  Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin , 2002, Nature Genetics.

[30]  Charles Kooperberg,et al.  The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. , 2004, Genes & development.

[31]  P. Brown,et al.  Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. , 2000, Molecular cell.

[32]  Yoshihide Hayashizaki,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 , 2006, Chromosome Research.

[33]  Kevin Struhl,et al.  Heterochromatin formation involves changes in histone modifications over multiple cell generations , 2005, The EMBO journal.

[34]  M. Grunstein,et al.  In vivo protein-protein and protein-DNA crosslinking for genomewide binding microarray. , 2003, Methods.

[35]  Pierre Chambon,et al.  NSD1 is essential for early post‐implantation development and has a catalytically active SET domain , 2003, The EMBO journal.

[36]  H. Szerlong,et al.  Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14 , 2004, The EMBO journal.

[37]  J. Tyler,et al.  Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. , 2004, Molecular cell.

[38]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

[39]  Alan P. Wolffe,et al.  Disruption of Higher-Order Folding by Core Histone Acetylation Dramatically Enhances Transcription of Nucleosomal Arrays by RNA Polymerase III , 1998, Molecular and Cellular Biology.

[40]  D. J. Clarke,et al.  Selective use of H4 acetylation sites in the yeast Saccharomyces cerevisiae. , 1993, The Biochemical journal.

[41]  Ming-Ming Zhou,et al.  Bromodomain: an acetyl‐lysine binding domain , 2002, FEBS letters.

[42]  J. Boeke,et al.  The Sirtuins Hst3 and Hst4p Preserve Genome Integrity by Controlling Histone H3 Lysine 56 Deacetylation , 2006, Current Biology.

[43]  Saeed Tavazoie,et al.  Genome-wide binding map of the histone deacetylase Rpd3 in yeast , 2002, Nature Genetics.

[44]  S. Gasser,et al.  A homotrimer-heterotrimer switch in Sir2 structure differentiates rDNA and telomeric silencing. , 2006, Molecular cell.

[45]  M. Grunstein,et al.  TUP1 utilizes histone H3/H2B-specific HDA1 deacetylase to repress gene activity in yeast. , 2001, Molecular cell.

[46]  C. Ponting,et al.  Regulation of chromatin structure by site-specific histone H3 methyltransferases , 2000, Nature.

[47]  M. Grunstein,et al.  Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast. , 2006, Genes & development.

[48]  Yi Zhang,et al.  Tudor, MBT and chromo domains gauge the degree of lysine methylation , 2006, EMBO reports.

[49]  D. Schübeler,et al.  Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias. , 2005, Genes & development.

[50]  S. Schreiber,et al.  Histone Variant H2A.Z Marks the 5′ Ends of Both Active and Inactive Genes in Euchromatin , 2006, Cell.

[51]  S. Buratowski,et al.  Bromodomain factor 1 corresponds to a missing piece of yeast TFIID. , 2000, Genes & development.

[52]  Amelia U. Santos‐Paulino,et al.  A Bird's Eye (Re)view , 2008 .

[53]  D. S. Gross,et al.  Domain-Wide Displacement of Histones by Activated Heat Shock Factor Occurs Independently of Swi/Snf and Is Not Correlated with RNA Polymerase II Density , 2005, Molecular and Cellular Biology.

[54]  Haico van Attikum,et al.  The histone code at DNA breaks: a guide to repair? , 2005, Nature Reviews Molecular Cell Biology.

[55]  M. Grunstein,et al.  Genomewide histone acetylation microarrays. , 2003, Methods.

[56]  J. Lieb,et al.  Evidence for nucleosome depletion at active regulatory regions genome-wide , 2004, Nature Genetics.

[57]  Neil L Kelleher,et al.  Precise characterization of human histones in the H2A gene family by top down mass spectrometry. , 2006, Journal of proteome research.

[58]  B. Turner,et al.  Histone H4 acetylation in human cells Frequency of acetylation at different sites defined by immunolabeling with site‐specific antibodies , 1989, FEBS letters.

[59]  Lisa Milne,et al.  Acetylation of the Yeast Histone H4 N Terminus Regulates Its Binding to Heterochromatin Protein SIR3* , 2002, The Journal of Biological Chemistry.

[60]  J. Broach,et al.  Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. , 1993, Genes & development.

[61]  S. Henikoff,et al.  The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. , 2002, Molecular cell.

[62]  Michael Grunstein,et al.  Requirement of Hos2 Histone Deacetylase for Gene Activity in Yeast , 2002, Science.

[63]  Philip R Gafken,et al.  Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4. , 2003, Analytical biochemistry.

[64]  J. Workman,et al.  Function and Selectivity of Bromodomains in Anchoring Chromatin-Modifying Complexes to Promoter Nucleosomes , 2002, Cell.

[65]  K. Ekwall,et al.  Genome-wide patterns of histone modifications in fission yeast , 2006, Chromosome Research.

[66]  Xiang Guo,et al.  Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae , 2006, Bioinform..

[67]  Nicola J. Rinaldi,et al.  Global position and recruitment of HATs and HDACs in the yeast genome. , 2004, Molecular cell.

[68]  Bing Li,et al.  Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription , 2005, Cell.

[69]  Song Tan,et al.  Yeast enhancer of polycomb defines global Esa1-dependent acetylation of chromatin. , 2003, Genes & development.

[70]  D. G. Gibson,et al.  The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae , 2004, Molecular and Cellular Biology.

[71]  Karl Mechtler,et al.  Protein phosphatase 2A protects centromeric sister chromatid cohesion during meiosis I , 2006, Nature.

[72]  Karl Ekwall,et al.  Genome wide analysis of nucleosome density histone acetylation and HDAC function in fission yeast , 2005, The EMBO journal.

[73]  D. Reinberg,et al.  Tips in analyzing antibodies directed against specific histone tail modifications. , 2004, Methods in enzymology.

[74]  B. Cairns,et al.  Genome-Wide Dynamics of Htz1, a Histone H2A Variant that Poises Repressed/Basal Promoters for Activation through Histone Loss , 2005, Cell.

[75]  Brian D. Strahl,et al.  Dimethylation of Histone H3 at Lysine 36 DemarcatesRegulatory and Nonregulatory ChromatinGenome-Wide , 2005, Molecular and Cellular Biology.

[76]  S. Buratowski,et al.  Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. , 2003, Molecular cell.

[77]  Kevin Struhl,et al.  Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. , 2003, Molecular cell.

[78]  Andreas Hecht,et al.  Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: A molecular model for the formation of heterochromatin in yeast , 1995, Cell.

[79]  Cyrus Martin,et al.  The diverse functions of histone lysine methylation , 2005, Nature Reviews Molecular Cell Biology.

[80]  M. Grunstein,et al.  Genetic evidence for an interaction between SIR3 and histone H4 in the repression of the silent mating loci in Saccharomyces cerevisiae. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[81]  Neil L Kelleher,et al.  Mass spectrometric characterization of human histone H3: a bird's eye view. , 2006, Journal of proteome research.

[82]  M. McVey,et al.  Sir2: an NAD-dependent histone deacetylase that connects chromatin silencing, metabolism, and aging. , 2000, Cold Spring Harbor symposia on quantitative biology.

[83]  Mathieu Blanchette,et al.  Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning , 2005, PLoS biology.

[84]  M. Grunstein.  Yeast Heterochromatin: Regulation of Its Assembly and Inheritance by Histones , 1998, Cell.

[85]  B. Turner,et al.  Histone H4 acetylation in Drosophila Frequency of acetylation at different sites defined by immunolabelling with site‐specific antibodies , 1991, FEBS letters.

[86]  Michael Grunstein,et al.  Histone H2B ubiquitylation controls processive methylation but not monomethylation by Dot1 and Set1. , 2005, Molecular cell.

[87]  Ioannis Xenarios,et al.  Microarray Deacetylation Maps Determine Genome-Wide Functions for Yeast Histone Deacetylases , 2002, Cell.

[88]  D. Koshland,et al.  Cse4p Is a Component of the Core Centromere of Saccharomyces cerevisiae , 1998, Cell.

[89]  A. Kimura,et al.  Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing , 2002, Nature Genetics.

[90]  A. Schmid,et al.  The Histone Chaperone Asf1 Increases the Rate of Histone Eviction at the Yeast PHO5 and PHO8 Promoters* , 2006, Journal of Biological Chemistry.

[91]  Nevan J. Krogan,et al.  Cotranscriptional Set2 Methylation of Histone H3 Lysine 36 Recruits a Repressive Rpd3 Complex , 2005, Cell.

[92]  R. Sternglanz,et al.  The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[93]  H. Reinke,et al.  Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. , 2003, Molecular cell.

[94]  Nancy L. Maas,et al.  Cell cycle and checkpoint regulation of histone H3 K56 acetylation by Hst3 and Hst4. , 2006, Molecular cell.

[95]  K. Srnuul,et al.  Activation and Repression Mechanisms in Yeast , 2008 .

[96]  David Hawke,et al.  A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response , 2005, Nature.

[97]  Thomas A. Milne,et al.  WDR5 Associates with Histone H3 Methylated at K4 and Is Essential for H3 K4 Methylation and Vertebrate Development , 2005, Cell.

[98]  T. Sugiyama,et al.  Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome , 2005, Nature Genetics.

[99]  R. Tjian,et al.  Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. , 2003, Molecular cell.

[100]  Eulàlia de Nadal,et al.  The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes , 2004, Nature.

[101]  Jerry L. Workman,et al.  Expanded Lysine Acetylation Specificity of Gcn5 in Native Complexes* , 1999, The Journal of Biological Chemistry.

[102]  M. Pazin,et al.  Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions , 2006, Science.

[103]  G. Karpen,et al.  Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin , 2004, Nature Structural &Molecular Biology.

[104]  Michael Grunstein,et al.  Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast , 1994, Nature.

[105]  Eric S. Lander,et al.  Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse , 2005, Cell.

[106]  Saeed Tavazoie,et al.  Mapping Global Histone Acetylation Patterns to Gene Expression , 2004, Cell.

[107]  S. Schreiber,et al.  Global nucleosome occupancy in yeast , 2004, Genome Biology.

[108]  D. Moazed,et al.  Sir2 Regulates Histone H3 Lysine 9 Methylation and Heterochromatin Assembly in Fission Yeast , 2003, Current Biology.

[109]  J. Hayes,et al.  Intra- and Inter-nucleosomal Protein-DNA Interactions of the Core Histone Tail Domains in a Model System* , 2003, Journal of Biological Chemistry.