Histone modifications: signalling receptors and potential elements of a heritable epigenetic code.

The genetic code epitomises simplicity, near universality and absolute predictive power. By contrast, epigenetic information, in the form of histone modifications, is characterised by complexity, diversity and an overall tendency to respond to changes in genomic function rather than to predict them. Perhaps the transient changes in histone modifications involved in intranuclear signalling and ongoing chromatin functions mask stable, predictive modifications that lie beneath. The current rapid progress in unravelling the diversity and complexity of epigenetic information might eventually reveal an underlying histone or epigenetic code. But whether it does or not, it will certainly provide unprecedented opportunities, both for understanding how the genome responds to environmental and metabolic change and for manipulating its activities for experimental and therapeutic benefit.

[1]  C. Bradbury,et al.  Histone deacetylases in acute myeloid leukaemia show a distinctive pattern of expression that changes selectively in response to deacetylase inhibitors , 2005, Leukemia.

[2]  Stormy J. Chamberlain,et al.  The Murine Polycomb Group Protein Eed Is Required for Global Histone H3 Lysine-27 Methylation , 2005, Current Biology.

[3]  Antoine H. F. M. Peters,et al.  LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription , 2005, Nature.

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

[5]  Tanja Waldmann,et al.  HP1 Binds Specifically to Lys26-methylated Histone H1.4, whereas Simultaneous Ser27 Phosphorylation Blocks HP1 Binding* , 2005, Journal of Biological Chemistry.

[6]  B. Strahl,et al.  Methylation of Histone H3 Lysine 36 Is Required for Normal Development in Neurospora crassa , 2005, Eukaryotic Cell.

[7]  Min Gyu Lee,et al.  An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation , 2005, Nature.

[8]  S. Henikoff,et al.  Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis , 2005, Genome Biology.

[9]  Wolf Reik,et al.  Co-evolution of X-chromosome inactivation and imprinting in mammals , 2005, Nature Reviews Genetics.

[10]  A. Shilatifard,et al.  Recruitment of MLL by HMG-domain protein iBRAF promotes neural differentiation , 2005, Nature Cell Biology.

[11]  Paul Tempst,et al.  Histone Deimination Antagonizes Arginine Methylation , 2004, Cell.

[12]  R. Allshire,et al.  Methylation: lost in hydroxylation? , 2005, EMBO reports.

[13]  F. Forneris,et al.  Human Histone Demethylase LSD1 Reads the Histone Code* , 2005, Journal of Biological Chemistry.

[14]  Danny Reinberg,et al.  Human but Not Yeast CHD1 Binds Directly and Selectively to Histone H3 Methylated at Lysine 4 via Its Tandem Chromodomains* , 2005, Journal of Biological Chemistry.

[15]  Steven Henikoff,et al.  Histone modifications: combinatorial complexity or cumulative simplicity? , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Brian D. Strahl,et al.  A Novel Domain in Set2 Mediates RNA Polymerase II Interaction and Couples Histone H3 K36 Methylation with Transcript Elongation , 2005, Molecular and Cellular Biology.

[17]  B. Turner Decoding the nucleosome , 1993, Cell.

[18]  Steven J Altschuler,et al.  Genomic characterization reveals a simple histone H4 acetylation code. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  M. Hung,et al.  Akt-Mediated Phosphorylation of EZH2 Suppresses Methylation of Lysine 27 in Histone H3 , 2005, Science.

[20]  Zu-Wen Sun,et al.  Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast , 2002, Nature.

[21]  C. Allis,et al.  Correlation Between Histone Lysine Methylation and Developmental Changes at the Chicken β-Globin Locus , 2001, Science.

[22]  A. Bird DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[23]  Y. Matsui,et al.  A histone H3 methyltransferase controls epigenetic events required for meiotic prophase , 2005, Nature.

[24]  A. Feinberg,et al.  The epigenetic progenitor origin of human cancer , 2006, Nature Reviews Genetics.

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

[26]  Chintamani,et al.  Qualitative and quantitative dermatoglyphic traits in patients with breast cancer: a prospective clinical study , 2007, BMC Cancer.

[27]  Tony Kouzarides,et al.  Spatial Distribution of Di- and Tri-methyl Lysine 36 of Histone H3 at Active Genes* , 2005, Journal of Biological Chemistry.

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

[29]  E. Thompson,et al.  Plasticity of histone modifications across the invertebrate to vertebrate transition: histone H3 lysine 4 trimethylation in heterochromatin , 2005, Chromosome Research.

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

[31]  Steven Clarke,et al.  Human PAD4 Regulates Histone Arginine Methylation Levels via Demethylimination , 2004, Science.

[32]  G. Felsenfeld,et al.  Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9 , 2004, The EMBO journal.

[33]  Dimitris Thanos,et al.  Deciphering the Transcriptional Histone Acetylation Code for a Human Gene , 2002, Cell.

[34]  H. Erdjument-Bromage,et al.  Histone demethylation by a family of JmjC domain-containing proteins , 2006, Nature.

[35]  Bradley R Cairns,et al.  Histone trimethylation by Set1 is coordinated by the RRM, autoinhibitory, and catalytic domains , 2005, The EMBO journal.

[36]  T. R. Hebbes,et al.  Histone acetylation and globin gene switching. , 1992, Nucleic acids research.

[37]  L. Puskás,et al.  Arginine Methylation Provides Epigenetic Transcription Memory for Retinoid-Induced Differentiation in Myeloid Cells , 2005, Molecular and Cellular Biology.

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

[39]  Benjamin A. Garcia,et al.  Regulation of HP1–chromatin binding by histone H3 methylation and phosphorylation , 2005, Nature.

[40]  G. Blobel,et al.  Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. , 2005, Molecular cell.

[41]  P. Grant,et al.  Effector Proteins for Methylated Histones: An Expanding Family , 2005, Cell cycle.

[42]  T. Tsukiyama,et al.  Two Distinct Mechanisms of Chromatin Interaction by the Isw2 Chromatin Remodeling Complex In Vivo , 2005, Molecular and Cellular Biology.

[43]  Elizabeth W Karlson,et al.  Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. , 2005, American journal of human genetics.

[44]  Thomas A. Milne,et al.  Physical Association and Coordinate Function of the H3 K4 Methyltransferase MLL1 and the H4 K16 Acetyltransferase MOF , 2005, Cell.

[45]  Kevin Struhl,et al.  Ubiquitination of Histone H2B by Rad6 Is Required for Efficient Dot1-mediated Methylation of Histone H3 Lysine 79* , 2002, The Journal of Biological Chemistry.

[46]  Ryuji Kobayashi,et al.  The Set1 Methyltransferase Opposes Ipl1 Aurora Kinase Functions in Chromosome Segregation , 2005, Cell.

[47]  A. Suzuki,et al.  Citrullinated proteins in rheumatoid arthritis. , 2005, Frontiers in bioscience : a journal and virtual library.

[48]  Heike Brand,et al.  Estrogen Receptor-α Directs Ordered, Cyclical, and Combinatorial Recruitment of Cofactors on a Natural Target Promoter , 2003, Cell.

[49]  S. Horvath,et al.  Global histone modification patterns predict risk of prostate cancer recurrence , 2005, Nature.

[50]  Anne E Carpenter,et al.  In Vivo HP1 Targeting Causes Large-Scale Chromatin Condensation and Enhanced Histone Lysine Methylation , 2005, Molecular and Cellular Biology.

[51]  J. Mellor,et al.  Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. , 2005, Molecular cell.

[52]  T. Jenuwein,et al.  Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3 , 2004, The EMBO journal.

[53]  M. Fraga,et al.  Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer , 2005, Nature Genetics.

[54]  P. Lichter,et al.  hMOF Histone Acetyltransferase Is Required for Histone H4 Lysine 16 Acetylation in Mammalian Cells , 2005, Molecular and Cellular Biology.

[55]  Y. Kochi,et al.  The inhibition of antithrombin by peptidylarginine deiminase 4 may contribute to pathogenesis of rheumatoid arthritis. , 2005, Rheumatology.

[56]  Renato Paro,et al.  Distinct contributions of histone H3 lysine 9 and 27 methylation to locus-specific stability of polycomb complexes. , 2004, Molecular cell.

[57]  Patrick England,et al.  Tethering of HP1 proteins to chromatin is relieved by phosphoacetylation of histone H3 , 2004, EMBO reports.

[58]  A. Bird,et al.  Female-specific hyperacetylation of histone H4 in the chicken Z chromosome , 2005, Chromosome Research.

[59]  R. Amasino,et al.  Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3 , 2004, Nature.

[60]  Yi Zhang,et al.  Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes , 2004, Nature Genetics.

[61]  T. Hughes,et al.  BUR Kinase Selectively Regulates H3 K4 Trimethylation and H2B Ubiquitylation through Recruitment of the PAF Elongation Complex , 2005, Current Biology.

[62]  Mark Johnston,et al.  Methylation of Histone H3 by COMPASS Requires Ubiquitination of Histone H2B by Rad6* , 2002, The Journal of Biological Chemistry.

[63]  G. Felsenfeld,et al.  Methylation of histone H4 by arginine methyltransferase PRMT1 is essential in vivo for many subsequent histone modifications. , 2005, Genes & development.

[64]  M. Stallcup,et al.  Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[65]  François Fuks,et al.  DNA methylation and histone modifications: teaming up to silence genes. , 2005, Current opinion in genetics & development.

[66]  Shireen A. Sarraf,et al.  Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. , 2004, Molecular cell.

[67]  Tony Kouzarides,et al.  Reversing histone methylation , 2005, Nature.

[68]  E. Valls,et al.  Role of Histone Modifications in Marking and Activating Genes through Mitosis* , 2005, Journal of Biological Chemistry.

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

[70]  B. Turner,et al.  Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei , 1992, Cell.

[71]  William Arbuthnot Sir Lane,et al.  A Human Protein Complex Homologous to the Drosophila MSL Complex Is Responsible for the Majority of Histone H4 Acetylation at Lysine 16 , 2005, Molecular and Cellular Biology.

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

[73]  Matthew Meyerson,et al.  The Menin Tumor Suppressor Protein Is an Essential Oncogenic Cofactor for MLL-Associated Leukemogenesis , 2005, Cell.

[74]  M. Grunstein,et al.  Acetylation of yeast histone H4 lysine 16: a switch for protein interactions in heterochromatin and euchromatin. , 2004, Cold Spring Harbor symposia on quantitative biology.

[75]  R. Martienssen,et al.  Vernalization requires epigenetic silencing of FLC by histone methylation , 2004, Nature.

[76]  R. Roeder,et al.  Ordered Cooperative Functions of PRMT1, p300, and CARM1 in Transcriptional Activation by p53 , 2004, Cell.

[77]  M. Yamada,et al.  Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes. , 2005, Biochemistry.

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

[79]  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.

[80]  B. Turner,et al.  Reading signals on the nucleosome with a new nomenclature for modified histones , 2005, Nature Structural &Molecular Biology.

[81]  E. Bradbury,et al.  A mass spectrometric “Western blot” to evaluate the correlations between histone methylation and histone acetylation , 2004, Proteomics.

[82]  K. Mitsuya,et al.  Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation , 2004, Nature Genetics.

[83]  F. Lan,et al.  Regulation of LSD1 histone demethylase activity by its associated factors. , 2005, Molecular cell.

[84]  Alain Verreault,et al.  Histone H3 lysine 4 mono-methylation does not require ubiquitination of histone H2B. , 2005, Journal of molecular biology.

[85]  A. Probst,et al.  Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis , 2005, The EMBO journal.

[86]  E. Ezhkova,et al.  Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3. , 2004, Molecular cell.

[87]  Paul Tempst,et al.  Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. , 2005, Molecular cell.

[88]  A. Shilatifard,et al.  Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression. , 2005, Molecular cell.

[89]  Jesse J. Lipp,et al.  Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin , 2005, Nature.

[90]  John R. Yates,et al.  Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation , 2005, Nature.

[91]  D. Reinberg,et al.  The key to development: interpreting the histone code? , 2005, Current opinion in genetics & development.

[92]  Ian M. Fingerman,et al.  Global Loss of Set1-mediated H3 Lys4 Trimethylation Is Associated with Silencing Defects in Saccharomyces cerevisiae* , 2005, Journal of Biological Chemistry.

[93]  A. Shilatifard,et al.  Cross-talking histones: implications for the regulation of gene expression and DNA repair. , 2005, Biochemistry and cell biology = Biochimie et biologie cellulaire.