Natural history of the eukaryotic chromatin protein methylation system

Progress in Molecular Biology and Translational Science

Volumn 101, Issue , 2011, Pages 105-176

  Aravind, L ^a   Abhiman, Saraswathi ^a   Iyer, Lakshminarayan M ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79955057405     PISSN: 18771173     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-387685-0.00004-4     Document Type: Chapter

References (267)

1. C.J. Dorman Nucleoid-associated proteins and bacterial physiology Adv Appl Microbiol 67 2009 47 64
2. L.B. Pedersen, S. Birkelund, and G. Christiansen Purification of recombinant Chlamydia trachomatis histone H1-like protein Hc2, and comparative functional analysis of Hc2 and Hc1 Mol Microbiol 20 1996 295 311 (Pubitemid 26141837)
3. E. Perara, D. Ganem, and J.N. Engel A developmentally regulated chlamydial gene with apparent homology to eukaryotic histone H1 Proc Natl Acad Sci USA 89 1992 2125 2129
4. J.N. Reeve, K.A. Bailey, W.T. Li, F. Marc, K. Sandman, and D.J. Soares Archaeal histones: structures, stability and DNA binding Biochem Soc Trans 32 2004 227 230 (Pubitemid 38582096)
5. L. Aravind, L.M. Iyer, and V. Anantharaman The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism Genome Biol 4 2003 R64
6. L. Aravind, L.M. Iyer, and E.V. Koonin Comparative genomics and structural biology of the molecular innovations of eukaryotes Curr Opin Struct Biol 16 2006 409 419 (Pubitemid 43831642)
7. V. Anantharaman, L.M. Iyer, and L. Aravind Comparative genomics of protists: new insights into the evolution of eukaryotic signal transduction and gene regulation Annu Rev Microbiol 61 2007 453 475 (Pubitemid 350058217)
8. L.M. Iyer, V. Anantharaman, M.Y. Wolf, and L. Aravind Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes Int J Parasitol 38 2008 1 31 (Pubitemid 350251386)
9. B.J. Mans, V. Anantharaman, L. Aravind, and E.V. Koonin Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex Cell Cycle 3 2004 1612 1637 (Pubitemid 40521416)
10. V. Anantharaman, E.V. Koonin, and L. Aravind Comparative genomics and evolution of proteins involved in RNA metabolism Nucleic Acids Res 30 2002 1427 1464 (Pubitemid 34679722)
11. E. Staub, P. Fiziev, A. Rosenthal, and B. Hinzmann Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire Bioessays 26 2004 567 581 (Pubitemid 38684972)
12. J. Liu, H. Tan, and B. Rost Loopy proteins appear conserved in evolution J Mol Biol 322 2002 53 64 (Pubitemid 36132670)
13. M. Rouleau, R.A. Aubin, and G.G. Poirier Poly(ADP-ribosyl)ated chromatin domains: access granted J Cell Sci 117 2004 815 825 (Pubitemid 38386940)
14. J. van Dijk, J. Miro, J.M. Strub, B. Lacroix, A. van Dorsselaer, and B. Edde Polyglutamylation is a post-translational modification with a broad range of substrates J Biol Chem 283 2008 3915 3922
15. T. Kouzarides Chromatin modifications and their function Cell 128 2007 693 705 (Pubitemid 46273577)
16. C.T. Walsh, S. Garneau-Tsodikova, and G.J. Gatto Protein posttranslational modifications: the chemistry of proteome diversifications Angew Chem 2005 2005 7342 7372 (Pubitemid 41689988)
17. C.D. Allis, T. Jenuwein, and D. Reinberg Epigenetics 2007 Cold Spring Harbor Laboratory Press Cold Spring Harbor, N.Y
18. C.I. Pereira, M.V. San Romao, J.S. Lolkema, and M.T. Crespo Weissella halotolerans W22 combines arginine deiminase and ornithine decarboxylation pathways and converts arginine to putrescine J Appl Microbiol 107 2009 1894 1902
19. P.R. Thompson, and W. Fast Histone citrullination by protein arginine deiminase: is arginine methylation a green light or a roadblock? ACS Chem Biol 1 2006 433 441
20. C.J. Webby, A. Wolf, N. Gromak, M. Dreger, H. Kramer, and B. Kessler Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing Science 325 2009 90 93
21. L. Aravind, and E.V. Koonin The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases Genome Biol 2 2001 RESEARCH0007
22. R. Fujiki, T. Chikanishi, W. Hashiba, H. Ito, I. Takada, and R.G. Roeder GlcNAcylation of a histone methyltransferase in retinoic-acid-induced granulopoiesis Nature 459 2009 455 459
23. A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, and Z. Wang High-resolution profiling of histone methylations in the human genome Cell 129 2007 823 837 (Pubitemid 46802390)
24. G. Hewawasam, M. Shivaraju, M. Mattingly, S. Venkatesh, S. Martin-Brown, and L. Florens Psh1 is an E3 ubiquitin ligase that targets the centromeric histone variant Cse4 Mol Cell 40 2010 444 454
25. P. Ranjitkar, M.O. Press, X. Yi, R. Baker, M.J. MacCoss, and S. Biggins An E3 ubiquitin ligase prevents ectopic localization of the centromeric histone H3 variant via the centromere targeting domain Mol Cell 40 2010 455 464
26. P. Trojer, J. Zhang, M. Yonezawa, A. Schmidt, H. Zheng, and T. Jenuwein Dynamic Histone H1 Isotype 4 Methylation and Demethylation by Histone Lysine Methyltransferase G9a/KMT1C and the Jumonji Domain-containing JMJD2/KDM4 Proteins J Biol Chem 284 2009 8395 8405
27. T. Jenuwein, and C.D. Allis Translating the histone code Science 293 2001 1074 1080 (Pubitemid 32758077)
28. R.N. Dutnall, S.T. Tafrov, R. Sternglanz, and V. Ramakrishnan Structure of the yeast histone acetyltransferase Hat1: insights into substrate specificity and implications for the Gcn5-related N-acetyltransferase superfamily Cold Spring Harb Symp Quant Biol 63 1998 501 507 (Pubitemid 29282194)
29. A.F. Neuwald, and D. Landsman GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein Trends Biochem Sci 22 1997 154 155 (Pubitemid 27199313)
30. A.M. Burroughs, K.N. Allen, D. Dunaway-Mariano, and L. Aravind Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes J Mol Biol 361 2006 1003 1034 (Pubitemid 44192587)
31. G. Blander, and L. Guarente The Sir2 family of protein deacetylases Annu Rev Biochem 73 2004 417 435 (Pubitemid 39050375)
32. D.D. Leipe, and D. Landsman Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily Nucleic Acids Res 25 1997 3693 3697 (Pubitemid 27390190)
33. A. Xiao, H. Li, D. Shechter, S.H. Ahn, L.A. Fabrizio, and H. Erdjument-Bromage WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity Nature 457 2009 57 62
34. A.M. Burroughs, L.M. Iyer, and L. Aravind Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation Proteins 75 2009 895 910
35. A.M. Burroughs, M. Jaffee, L.M. Iyer, and L. Aravind Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation J Struct Biol 162 2008 205 218
36. A.M. Burroughs, S. Balaji, L.M. Iyer, and L. Aravind Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold Biol Direct 2 2007 18
37. J.M. Bujnicki Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation In Silico Biol 1 1999 175 182
38. H.L. Schubert, R.M. Blumenthal, and X. Cheng Many paths to methyltransfer: a chronicle of convergence Trends Biochem Sci 28 2003 329 335 (Pubitemid 36776296)
39. E.B. Fauman, RM Blumenthal, and X. Cheng Structure and evolution of AdoMet-dependent methyltransferases X. Cheng, R.M. Blumenthal, S-adeno-sylmethionine-dependent methyltransferases: Structures and functions 1999 1 54 River Edge: World Scientific
40. L.M. Iyer, and L. Aravind The emergence of catalytic and structural diversity within the beta-clip fold Proteins 55 2004 977 991 (Pubitemid 38702954)
41. R.S. Lipson, K.J. Webb, and S.G. Clarke Two novel methyltransferases acting upon eukaryotic elongation factor 1A in Saccharomyces cerevisiae Arch Biochem Biophys 500 2010 137 143
42. T.R. Porras-Yakushi, J.P. Whitelegge, and S. Clarke Yeast ribosomal/cytochrome c SET domain methyltransferase subfamily: identification of Rpl23ab methylation sites and recognition motifs J Biol Chem 282 2007 12368 12376 (Pubitemid 47100580)
43. T.R. Porras-Yakushi, J.P. Whitelegge, T.B. Miranda, and S. Clarke A novel SET domain methyltransferase modifies ribosomal protein Rpl23ab in yeast J Biol Chem 280 2005 34590 34598 (Pubitemid 41504589)
44. M. Sadaie, K. Shinmyozu, and J. Nakayama A conserved SET domain methyltransferase, Set11, modifies ribosomal protein Rpl12 in fission yeast J Biol Chem 283 2008 7185 7195
45. M.R. Martzen, S.M. McCraith, S.L. Spinelli, F.M. Torres, S. Fields, and E.J. Grayhack A biochemical genomics approach for identifying genes by the activity of their products Science 286 1999 1153 1155
46. P.Z. Kozbial, and A.R. Mushegian Natural history of S-adenosylmethionine- binding proteins BMC Struct Biol 5 2005 19
47. V. Heurgue-Hamard, S. Champ, A. Engstrom, M. Ehrenberg, and R.H. Buckingham The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors EMBO J 21 2002 769 778 (Pubitemid 34174057)
48. K. Nakahigashi, N. Kubo, S. Narita, T. Shimaoka, S. Goto, and T. Oshima HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination Proc Natl Acad Sci USA 99 2002 1473 1478 (Pubitemid 34136517)
49. H. Demirci, S.T. Gregory, A.E. Dahlberg, and G. Jogl Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase Structure 16 2008 1059 1066 (Pubitemid 351899284)
50. Y.H. Lee, and M.R. Stallcup Minireview: protein arginine methylation of nonhistone proteins in transcriptional regulation Mol Endocrinol 23 2009 425 433
51. S. Pal, and S. Sif Interplay between chromatin remodelers and protein arginine methyltransferases J Cell Physiol 213 2007 306 315 (Pubitemid 47509707)
52. W. An, J. Kim, and R.G. Roeder Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53 Cell 117 2004 735 748 (Pubitemid 38748890)
53. S.A. Blythe, S.W. Cha, E. Tadjuidje, J. Heasman, and P.S. Klein beta-Catenin primes organizer gene expression by recruiting a histone H3 arginine 8 methyltransferase, Prmt2 Dev Cell 19 2010 220 231
54. S.L. Chen, K.A. Loffler, D. Chen, M.R. Stallcup, and G.E. Muscat The coactivator-associated arginine methyltransferase is necessary for muscle differentiation: CARM1 coactivates myocyte enhancer factor-2 J Biol Chem 277 2002 4324 4333 (Pubitemid 34968698)
55. T.M. Lakowski, and A. Frankel Kinetic analysis of human protein arginine N-methyltransferase 2: formation of monomethyl- and asymmetric dimethyl-arginine residues on histone H4 Biochem J 421 2009 253 261
56. B.D. Strahl, S.D. Briggs, C.J. Brame, J.A. Caldwell, S.S. Koh, and H. Ma Methylation of histone H4 at arginine 3 occurs in vivo and is mediated by the nuclear receptor coactivator PRMT1 Curr Biol 11 2001 996 1000 (Pubitemid 32589194)
57. H. Wang, Z.Q. Huang, L. Xia, Q. Feng, H. Erdjument-Bromage, and B.D. Strahl Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor Science 293 2001 853 857 (Pubitemid 32743973)
58. W.W. Yue, M. Hassler, S.M. Roe, V. Thompson-Vale, and L.H. Pearl Insights into histone code syntax from structural and biochemical studies of CARM1 methyltransferase EMBO J 26 2007 4402 4412 (Pubitemid 47587659)
59. T.B. Miranda, K.J. Webb, D.D. Edberg, R. Reeves, and S. Clarke Protein arginine methyltransferase 6 specifically methylates the nonhistone chromatin protein HMGA1a Biochem Biophys Res Commun 336 2005 831 835 (Pubitemid 41338343)
60. J. Anne, R. Ollo, A. Ephrussi, and B.M. Mechler Arginine methyltransferase Capsuleen is essential for methylation of spliceosomal Sm proteins and germ cell formation in Drosophila Development 134 2007 137 146 (Pubitemid 46152714)
61. J.Y. Chan, T.Y. Hsieh, S.T. Liu, W.Y. Chou, M.H. Chung, and S.M. Huang Physical and functional interactions between hnRNP K and PRMT family proteins FEBS Lett 583 2009 281 286
62. G.B. Gonsalvez, L. Tian, J.K. Ospina, F.M. Boisvert, A.I. Lamond, and A.G. Matera Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins J Cell Biol 178 2007 733 740 (Pubitemid 47347358)
63. C. Kim, Y. Lim, B.C. Yoo, N.H. Won, S. Kim, and G. Kim Regulation of post-translational protein arginine methylation during HeLa cell cycle Biochim Biophys Acta 1800 2010 977 985
64. S. Pahlich, R.P. Zakaryan, and H. Gehring Identification of proteins interacting with protein arginine methyltransferase 8: the Ewing sarcoma (EWS) protein binds independent of its methylation state Proteins 72 2008 1125 1137
65. V.V. Vagin, J. Wohlschlegel, J. Qu, Z. Jonsson, X. Huang, and S. Chuma Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members Genes Dev 23 2009 1749 1762
66. F. Bachand, and P.A. Silver PRMT3 is a ribosomal protein methyltransferase that affects the cellular levels of ribosomal subunits EMBO J 23 2004 2641 2650 (Pubitemid 38988235)
67. L. Niu, F. Lu, Y. Pei, C. Liu, and X. Cao Regulation of flowering time by the protein arginine methyltransferase AtPRMT10 EMBO Rep 8 2007 1190 1195 (Pubitemid 350201739)
68. J.C. Fisk, J. Sayegh, C. Zurita-Lopez, S. Menon, V. Presnyak, and S.G. Clarke A type III protein arginine methyltransferase from the protozoan parasite Trypanosoma brucei J Biol Chem 284 2009 11590 11600
69. N. Troffer-Charlier, V. Cura, P. Hassenboehler, D. Moras, and J. Cavarelli Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains EMBO J 26 2007 4391 4401 (Pubitemid 47587658)
70. J.H. Lee, J.R. Cook, Z.H. Yang, O. Mirochnitchenko, S.I. Gunderson, and A.M. Felix PRMT7, a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine J Biol Chem 280 2005 3656 3664 (Pubitemid 40223833)
71. A. Frankel, and S. Clarke PRMT3 is a distinct member of the protein arginine N-methyltransferase family Conferral of substrate specificity by a zinc-finger domain. J Biol Chem 275 2000 32974 32982
72. L. Rouhiainen, L. Paulin, S. Suomalainen, H. Hyytiainen, W. Buikema, and R. Haselkorn Genes encoding synthetases of cyclic depsipeptides, anabaenopeptilides, in Anabaena strain 90 Mol Microbiol 37 2000 156 167 (Pubitemid 30479365)
73. J. Mellor Linking the cell cycle to histone modifications: DOT1, G1/S, and cycling K79me2 Mol Cell 35 2009 729 730
74. Y. Okada, Q. Feng, Y. Lin, Q. Jiang, Y. Li, and V.M. Coffield hDOT1L links histone methylation to leukemogenesis Cell 121 2005 167 178 (Pubitemid 40546386)
75. Q. Feng, H. Wang, H.H. Ng, H. Erdjument-Bromage, P. Tempst, and K. Struhl Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain Curr Biol 12 2002 1052 1058 (Pubitemid 34703339)
76. M. Dlakic Chromatin silencing protein and pachytene checkpoint regulator DOT1p has a methyltransferase fold Trends Biochem Sci 26 2001 405 407 (Pubitemid 32607475)
77. J.M. Schulze, J. Jackson, S. Nakanishi, J.M. Gardner, T. Hentrich, and J. Haug Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation Mol Cell 35 2009 626 641
78. W. Zhang, Y. Hayashizaki, and B.C. Kone Structure and regulation of the mDOT1 gene, a mouse histone H3 methyltransferase Biochem J 377 2004 641 651 (Pubitemid 38221835)
79. S. Oh, K. Jeong, H. Kim, C.S. Kwon, and D. Lee A lysine-rich region in DOT1p is crucial for direct interaction with H2B ubiquitylation and high level methylation of H3K79 Biochem Biophys Res Commun 399 2010 512 517
80. F. Frederiks, T. van Welsem, G. Oudgenoeg, A.J. Heck, C.J. Janzen, and F. van Leeuwen Heterologous expression reveals distinct enzymatic activities of two DOT1 histone methyltransferases of Trypanosoma brucei J Cell Sci 123 2010 4019 4023
81. N. Levesque, G.P. Leung, A.K. Fok, T.I. Schmidt, and M.S. Kobor Loss of H3 K79 trimethylation leads to suppression of Rtt107-dependent DNA damage sensitivity through the translesion synthesis pathway J Biol Chem 285 2010 35113 35122
82. F. Conde, and P.A. San-Segundo Role of DOT1 in the response to alkylating DNA damage in Saccharomyces cerevisiae: regulation of DNA damage tolerance by the error-prone polymerases Polzeta/Rev1 Genetics 179 2008 1197 1210
83. F. Boissier, F. Bardou, V. Guillet, S. Uttenweiler-Joseph, M. Daffe, and A. Quemard Further insight into S-adenosylmethionine-dependent methyltransferases: structural characterization of Hma, an enzyme essential for the biosynthesis of oxygenated mycolic acids in Mycobacterium tuberculosis J Biol Chem 281 2006 4434 4445 (Pubitemid 43847875)
84. B.M. Harvey, T. Mironenko, Y. Sun, H. Hong, Z. Deng, and P.F. Leadlay Insights into polyether biosynthesis from analysis of the nigericin biosynthetic gene cluster in Streptomyces sp. DSM4137 Chem Biol 14 2007 703 714 (Pubitemid 46920987)
85. E.J. Richards, and S.C. Elgin Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects Cell 108 2002 489 500 (Pubitemid 34260874)
86. E.V. Koonin, L. Aravind, and A.S. Kondrashov The impact of comparative genomics on our understanding of evolution Cell 101 2000 573 576
87. T. Nakamura, T. Mori, S. Tada, W. Krajewski, T. Rozovskaia, and R. Wassell ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation Mol Cell 10 2002 1119 1128 (Pubitemid 35453829)
88. C. Beisel, A. Imhof, J. Greene, E. Kremmer, and F. Sauer Histone methylation by the Drosophila epigenetic transcriptional regulator Ash1 Nature 419 2002 857 862 (Pubitemid 35238574)
89. H. Wang, R. Cao, L. Xia, H. Erdjument-Bromage, C. Borchers, and P. Tempst Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase Mol Cell 8 2001 1207 1217 (Pubitemid 34084993)
90. P.O. Esteve, Y. Chang, M. Samaranayake, A.K. Upadhyay, J.R. Horton, and G.R. Feehery A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability Nat Struct Mol Biol 18 2011 42 48
91. J.F. Couture, E. Collazo, G. Hauk, and R.C. Trievel Structural basis for the methylation site specificity of SET7/9 Nat Struct Mol Biol 13 2006 140 146 (Pubitemid 43214717)
92. N. Sirinupong, J. Brunzelle, J. Ye, A. Pirzada, L. Nico, and Z. Yang Crystal structure of cardiac-specific histone methyltransferase SmyD1 reveals unusual active site architecture J Biol Chem 285 2010 40635 40644
93. S.D. Briggs, M. Bryk, B.D. Strahl, W.L. Cheung, J.K. Davie, and S.Y. Dent Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae Genes Dev 15 2001 3286 3295 (Pubitemid 34008193)
94. A. Saleh, A. Al-Abdallat, I. Ndamukong, R. Alvarez-Venegas, and Z. Avramova The Arabidopsis homologs of trithorax (ATX1) and enhancer of zeste (CLF) establish 'bivalent chromatin marks' at the silent AGAMOUS locus Nucleic Acids Res 35 2007 6290 6296 (Pubitemid 350018590)
95. K. Zhang, K. Mosch, W. Fischle, and S.I. Grewal Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin Nat Struct Mol Biol 15 2008 381 388 (Pubitemid 351483395)
96. J. Nakayama, J.C. Rice, B.D. Strahl, C.D. Allis, and S.I. Grewal Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly Science 292 2001 110 113 (Pubitemid 32289138)
97. K. Naumann, A. Fischer, I. Hofmann, V. Krauss, S. Phalke, and K. Irmler Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis EMBO J 24 2005 1418 1429 (Pubitemid 40593062)
98. C. Derunes, K. Briknarova, L. Geng, S. Li, C.R. Gessner, and K. Hewitt Characterization of the PR domain of RIZ1 histone methyltransferase Biochem Biophys Res Commun 333 2005 925 934 (Pubitemid 40854246)
99. R. Margueron, G. Li, K. Sarma, A. Blais, J. Zavadil, and C.L. Woodcock Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms Mol Cell 32 2008 503 518
100. M. Nekrasov, B. Wild, and J. Muller Nucleosome binding and histone methyltransferase activity of Drosophila PRC2 EMBO Rep 6 2005 348 353 (Pubitemid 40561627)
101. J. Muller, C.M. Hart, N.J. Francis, M.L. Vargas, A. Sengupta, and B. Wild Histone methyltransferase activity of a Drosophila Polycomb group repressor complex Cell 111 2002 197 208 (Pubitemid 35292440)
102. Y. Jacob, H. Stroud, C. Leblanc, S. Feng, L. Zhuo, and E. Caro Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases Nature 466 2010 987 991
103. M.A. Brown, R.J. Sims 3rd, P.D. Gottlieb, and P.W. Tucker Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex Mol Cancer 5 2006 26
104. B. Rao, Y. Shibata, B.D. Strahl, and J.D. Lieb Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide Mol Cell Biol 25 2005 9447 9459 (Pubitemid 41507845)
105. L. Balakrishnan, and B. Milavetz Decoding the histone H4 lysine 20 methylation mark Crit Rev Biochem Mol Biol 45 2010 440 452
106. G.V. Rayasam, O. Wendling, P.O. Angrand, M. Mark, K. Niederreither, and L. Song NSD1 is essential for early post-implantation development and has a catalytically active SET domain EMBO J 22 2003 3153 3163 (Pubitemid 36758635)
107. G.J. Filion, J.G. van Bemmel, U. Braunschweig, W. Talhout, J. Kind, and L.D. Ward Systematic protein location mapping reveals five principal chromatin types in Drosophila cells Cell 143 2010 212 224
108. T.A. Milne, S.D. Briggs, H.W. Brock, M.E. Martin, D. Gibbs, and C.D. Allis MLL targets SET domain methyltransferase activity to Hox gene promoters Mol Cell 10 2002 1107 1117 (Pubitemid 35453828)
109. T. Sanchez-Elsner, D. Gou, E. Kremmer, and F. Sauer Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax Science 311 2006 1118 1123
110. F. Baudat, J. Buard, C. Grey, A. Fledel-Alon, C. Ober, and M. Przeworski PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice Science 327 2010 836 840
111. S. Myers, R. Bowden, A. Tumian, R.E. Bontrop, C. Freeman, and T.S. MacFie Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination Science 327 2010 876 879
112. L. Xu, Z. Zhao, A. Dong, L. Soubigou-Taconnat, J.P. Renou, and A. Steinmetz Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana Mol Cell Biol 28 2008 1348 1360 (Pubitemid 351214136)
113. S.M. Yoh, J.S. Lucas, and K.A. Jones The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation Genes Dev 22 2008 3422 3434
114. S. Fnu, E.A. Williamson, L.P. De Haro, M. Brenneman, J. Wray, and M. Shaheen Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining Proc Natl Acad Sci USA 108 2011 540 545
115. M.S. Huen, S.M. Sy, J.M. van Deursen, and J. Chen Direct interaction between SET8 and proliferating cell nuclear antigen couples H4-K20 methylation with DNA replication J Biol Chem 283 2008 11073 11077
116. D. Kim, B.J. Blus, V. Chandra, P. Huang, F. Rastinejad, and S. Khorasanizadeh Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain Nat Struct Mol Biol 17 2010 1027 1029
117. E. Larschan, A.A. Alekseyenko, A.A. Gortchakov, S. Peng, B. Li, and P. Yang MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism Mol Cell 28 2007 121 133 (Pubitemid 47531971)
118. L. Aravind, and L.M. Iyer Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit Cell Cycle 2 2003 369 376
119. R.C. Trievel, B.M. Beach, L.M. Dirk, R.L. Houtz, and J.H. Hurley Structure and catalytic mechanism of a SET domain protein methyltransferase Cell 111 2002 91 103
120. S.A. Jacobs, J.M. Harp, S. Devarakonda, Y. Kim, F. Rastinejad, and S. Khorasanizadeh The active site of the SET domain is constructed on a knot Nat Struct Biol 9 2002 833 838 (Pubitemid 35257783)
121. T. Kwon, J.H. Chang, E. Kwak, C.W. Lee, A. Joachimiak, and Y.C. Kim Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet EMBO J 22 2003 292 303 (Pubitemid 36119435)
122. K.L. Manzur, A. Farooq, L. Zeng, O. Plotnikova, A.W. Koch, and Sachchidanand A dimeric viral SET domain methyltransferase specific to Lys27 of histone H3 Nat Struct Biol 10 2003 187 196 (Pubitemid 36297988)
123. J.R. Wilson, C. Jing, P.A. Walker, S.R. Martin, S.A. Howell, and G.M. Blackburn Crystal structure and functional analysis of the histone methyltransferase SET7/9 Cell 111 2002 105 115
124. X. Zhang, H. Tamaru, S.I. Khan, J.R. Horton, L.J. Keefe, and E.U. Selker Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase Cell 111 2002 117 127
125. B. Xiao, C. Jing, J.R. Wilson, P.A. Walker, N. Vasisht, and G. Kelly Structure and catalytic mechanism of the human histone methyltransferase SET7/9 Nature 421 2003 652 656 (Pubitemid 36227675)
126. L. Aravind, H. Watanabe, D.J. Lipman, and E.V. Koonin Lineage-specific loss and divergence of functionally linked genes in eukaryotes Proc Natl Acad Sci USA 97 2000 11319 11324
127. R.J. Klose, K.E. Gardner, G. Liang, H. Erdjument-Bromage, P. Tempst, and Y. Zhang Demethylation of histone H3K36 and H3K9 by Rph1: a vestige of an H3K9 methylation system in Saccharomyces cerevisiae? Mol Cell Biol 27 2007 3951 3961 (Pubitemid 47010993)
128. Y. Jacob, S. Feng, C.A. LeBlanc, Y.V. Bernatavichute, H. Stroud, and S. Cokus ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing Nat Struct Mol Biol 16 2009 763 768
129. M.M. Brent, and R. Marmorstein Ankyrin for methylated lysines Nat Struct Mol Biol 15 2008 221 222 (Pubitemid 351654053)
130. R.E. Collins, J.P. Northrop, J.R. Horton, D.Y. Lee, X. Zhang, and M.R. Stallcup The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules Nat Struct Mol Biol 15 2008 245 250 (Pubitemid 351654039)
131. C. Miskey, B. Papp, L. Mates, L. Sinzelle, H. Keller, and Z. Izsvak The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends Mol Cell Biol 27 2007 4589 4600 (Pubitemid 46906579)
132. M. Shaheen, E. Williamson, J. Nickoloff, S.H. Lee, and R. Hromas Metnase/SETMAR: a domesticated primate transposase that enhances DNA repair, replication, and decatenation Genetica 138 2010 559 566
133. T.N. Siegel, D.R. Hekstra, L.E. Kemp, L.M. Figueiredo, J.E. Lowell, and D. Fenyo Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei Genes Dev 23 2009 1063 1076
134. V. Mandava, C.J. Janzen, and G.A. Cross Trypanosome H2Bv replaces H2B in nucleosomes enriched for H3 K4 and K76 trimethylation Biochem Biophys Res Commun 368 2008 846 851
135. P.K. Lu, J.Y. Tsai, H.Y. Chien, H. Huang, C.H. Chu, and Y.J. Sun Crystal structure of Helicobacter pylori spermidine synthase: a Rossmann-like fold with a distinct active site Proteins 67 2007 743 754 (Pubitemid 46625589)
136. N. Kroger, R. Deutzmann, and M. Sumper Polycationic peptides from diatom biosilica that direct silica nanosphere formation Science 286 1999 1129 1132
137. M. Sumper, R. Hett, G. Lehmann, and S. Wenzl A code for lysine modifications of a silica biomineralizing silaffin protein Angew Chem Int Ed Engl 46 2007 8405 8408 (Pubitemid 350114949)
138. N. Kroger, S. Lorenz, E. Brunner, and M. Sumper Self-assembly of highly phosphorylated silaffins and their function in biosilica morphogenesis Science 298 2002 584 586 (Pubitemid 35215309)
139. V. Sheppard, N. Poulsen, and N. Kroger Characterization of an endoplasmic reticulum-associated silaffin kinase from the diatom Thalassiosira pseudonana J Biol Chem 285 2010 1166 1176
140. A. Boulton, R.S. Myers, and R.J. Redfield The hotspot conversion paradox and the evolution of meiotic recombination Proc Natl Acad Sci USA 94 1997 8058 8063 (Pubitemid 27343776)
141. R.S. Stephens, S. Kalman, C. Lammel, J. Fan, R. Marathe, and L. Aravind Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis Science 282 1998 754 759 (Pubitemid 28489390)
142. M.E. Pennini, S. Perrinet, A. Dautry-Varsat, and A. Subtil Histone methylation by NUE, a novel nuclear effector of the intracellular pathogen Chlamydia trachomatis PLoS Pathog 6 2010 e1000995
143. M. Murata, Y. Azuma, K. Miura, M.A. Rahman, M. Matsutani, and M. Aoyama Chlamydial SET domain protein functions as a histone methyltransferase Microbiology 153 2007 585 592
144. K.L. Manzur, and M.M. Zhou An archaeal SET domain protein exhibits distinct lysine methyltransferase activity towards DNA-associated protein MC1-alpha FEBS Lett 579 2005 3859 3865 (Pubitemid 40897736)
145. P.W. Hsiao, C.J. Fryer, K.W. Trotter, W. Wang, and T.K. Archer BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation Mol Cell Biol 23 2003 6210 6220 (Pubitemid 37013098)
146. T. Ito, M. Yamauchi, M. Nishina, N. Yamamichi, T. Mizutani, and M. Ui Identification of SWI.SNF complex subunit BAF60a as a determinant of the transactivation potential of Fos/Jun dimers J Biol Chem 276 2001 2852 2857
147. J. Oh, D.H. Sohn, M. Ko, H. Chung, S.H. Jeon, and R.H. Seong BAF60a interacts with p53 to recruit the SWI/SNF complex J Biol Chem 283 2008 11924 11934
148. R.F. de Souza, L.M. Iyer, and L. Aravind Diversity and evolution of chromatin proteins encoded by DNA viruses Biochim Biophys Acta 1799 2010 302 318
149. S. Mujtaba, K.L. Manzur, J.R. Gurnon, M. Kang, J.L. Van Etten, and M.M. Zhou Epigenetic transcriptional repression of cellular genes by a viral SET protein 2008 Nat Cell Biol
150. T. Hagiwara, K. Nakashima, H. Hirano, T. Senshu, and M. Yamada Deimination of arginine residues in nucleophosmin/B23 and histones in HL-60 granulocytes Biochem Biophys Res Commun 290 2002 979 983 (Pubitemid 34687458)
151. Y. Wang, J. Wysocka, J. Sayegh, Y.H. Lee, J.R. Perlin, and L. Leonelli Human PAD4 regulates histone arginine methylation levels via demethylimination Science 306 2004 279 283 (Pubitemid 39336873)
152. G.L. Cuthbert, S. Daujat, A.W. Snowden, H. Erdjument-Bromage, T. Hagiwara, and M. Yamada Histone deimination antagonizes arginine methylation Cell 118 2004 545 553 (Pubitemid 39179708)
153. E.R. Vossenaar, A.J. Zendman, W.J. van Venrooij, and G.J. Pruijn PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease Bioessays 25 2003 1106 1118 (Pubitemid 37411770)
154. Y.H. Lee, S.A. Coonrod, W.L. Kraus, M.A. Jelinek, and M.R. Stallcup Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination Proc Natl Acad Sci USA 102 2005 3611 3616 (Pubitemid 40354659)
155. P.L. Kearney, M. Bhatia, N.G. Jones, L. Yuan, M.C. Glascock, and K.L. Catchings Kinetic characterization of protein arginine deiminase 4: a transcriptional corepressor implicated in the onset and progression of rheumatoid arthritis Biochemistry 44 2005 10570 10582 (Pubitemid 41098234)
156. H. Shirai, T.L. Blundell, and K. Mizuguchi A novel superfamily of enzymes that catalyze the modification of guanidino groups Trends Biochem Sci 26 2001 465 468 (Pubitemid 32735442)
157. W.T. McGraw, J. Potempa, D. Farley, and J. Travis Purification, characterization, and sequence analysis of a potential virulence factor from Porphyromonas gingivalis, peptidylarginine deiminase Infect Immun 67 1999 3248 3256 (Pubitemid 29291488)
158. K. Arita, H. Hashimoto, T. Shimizu, K. Nakashima, M. Yamada, and M. Sato Structural basis for Ca(2+)-induced activation of human PAD4 Nat Struct Mol Biol 11 2004 777 783 (Pubitemid 39014504)
159. X. Lu, A. Galkin, O. Herzberg, and D. Dunaway-Mariano Arginine deiminase uses an active-site cysteine in nucleophilic catalysis of L-arginine hydrolysis J Am Chem Soc 126 2004 5374 5375 (Pubitemid 38596346)
160. M.C. Touz, A.S. Ropolo, M.R. Rivero, C.V. Vranych, J.T. Conrad, and S.G. Svard Arginine deiminase has multiple regulatory roles in the biology of Giardia lamblia J Cell Sci 121 2008 2930 2938
161. L. Aravind, and L.M. Iyer The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities Genome Biol 3 2002 RESEARCH0039
162. G.W. Humphrey, Y. Wang, V.R. Russanova, T. Hirai, J. Qin, and Y. Nakatani Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1 J Biol Chem 276 2001 6817 6824
163. T.B. Nicholson, and T. Chen LSD1 demethylates histone and non-histone proteins Epigenetics 4 2009 129 132
164. Y. Shi, F. Lan, C. Matson, P. Mulligan, J.R. Whetstine, and P.A. Cole Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 Cell 119 2004 941 953 (Pubitemid 40037608)
165. J.C. Culhane, and P.A. Cole LSD1 and the chemistry of histone demethylation Curr Opin Chem Biol 11 2007 561 568 (Pubitemid 47588999)
166. F. Forneris, C. Binda, E. Battaglioli, and A. Mattevi LSD1: oxidative chemistry for multifaceted functions in chromatin regulation Trends Biochem Sci 33 2008 181 189
167. T. Rudolph, M. Yonezawa, S. Lein, K. Heidrich, S. Kubicek, and C. Schafer Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU(VAR)3-3 Mol Cell 26 2007 103 115 (Pubitemid 46566423)
168. M.C. Tsai, O. Manor, Y. Wan, N. Mosammaparast, J.K. Wang, and F. Lan Long noncoding RNA as modular scaffold of histone modification complexes Science 329 2010 689 693
169. J. Wang, K. Scully, X. Zhu, L. Cai, J. Zhang, and G.G. Prefontaine Opposing LSD1 complexes function in developmental gene activation and repression programmes Nature 446 2007 882 887 (Pubitemid 46633160)
170. Y. Wang, H. Zhang, Y. Chen, Y. Sun, F. Yang, and W. Yu LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer Cell 138 2009 660 672
171. M. Gordon, D.G. Holt, A. Panigrahi, B.T. Wilhelm, H. Erdjument-Bromage, and P. Tempst Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries Mol Cell Biol 27 2007 4058 4069 (Pubitemid 47011003)
172. J. Huang, R. Sengupta, A.B. Espejo, M.G. Lee, J.A. Dorsey, and M. Richter p53 is regulated by the lysine demethylase LSD1 Nature 449 2007 105 108 (Pubitemid 47373772)
173. D.J. Katz, T.M. Edwards, V. Reinke, and W.G. Kelly A C. elegans LSD1 demethylase contributes to germline immortality by reprogramming epigenetic memory Cell 137 2009 308 320
174. T. Swigut, and J. Wysocka Fallen immortals Cell 137 2009 203 205
175. M. Yang, C.B. Gocke, X. Luo, D. Borek, D.R. Tomchick, and M. Machius Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase Mol Cell 23 2006 377 387 (Pubitemid 44128856)
176. F. Forneris, C. Binda, A. Adamo, E. Battaglioli, and A. Mattevi Structural basis of LSD1-CoREST selectivity in histone H3 recognition J Biol Chem 282 2007 20070 20074 (Pubitemid 47099979)
177. Y. Chen, Y. Yang, F. Wang, K. Wan, K. Yamane, and Y. Zhang Crystal structure of human histone lysine-specific demethylase 1 (LSD1) Proc Natl Acad Sci USA 103 2006 13956 13961 (Pubitemid 44452964)
178. T. Cook, D. Roos, M. Morada, G. Zhu, J.S. Keithly, and J.E. Feagin Divergent polyamine metabolism in the Apicomplexa Microbiology 153 2007 1123 1130 (Pubitemid 46605810)
179. S. Vujcic, P. Liang, P. Diegelman, D.L. Kramer, and C.W. Porter Genomic identification and biochemical characterization of the mammalian polyamine oxidase involved in polyamine back-conversion Biochem J 370 2003 19 28 (Pubitemid 36259415)
180. N. Seiler Catabolism of polyamines Amino Acids 26 2004 217 233 (Pubitemid 38829785)
181. L.M. Iyer, S. Abhiman, A. Maxwell Burroughs, and L. Aravind Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins Mol Biosyst 5 2009 1636 1660
182. L.M. Iyer, S. Abhiman, R.F. de Souza, and L. Aravind Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase Nucleic Acids Res 38 2010 5261 5279
183. T. Murray-Stewart, Y. Wang, A. Goodwin, A. Hacker, A. Meeker, and R.A. Casero Jr. Nuclear localization of human spermine oxidase isoforms - possible implications in drug response and disease etiology FEBS J 275 2008 2795 2806 (Pubitemid 351678666)
184. J. Larsson, J. Zhang, and A. Rasmuson-Lestander Mutations in the Drosophila melanogaster gene encoding S-adenosylmethionine synthetase [corrected] suppress position-effect variegation Genetics 143 1996 887 896
185. V. Anantharaman, E.V. Koonin, and L. Aravind Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains J Mol Biol 307 2001 1271 1292 (Pubitemid 33027639)
186. P.M. Clissold, and C.P. Ponting JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta Trends Biochem Sci 26 2001 7 9 (Pubitemid 32124697)
187. J.R. Whetstine, A. Nottke, F. Lan, M. Huarte, S. Smolikov, and Z. Chen Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases Cell 125 2006 467 481
188. Y. Tsukada, J. Fang, H. Erdjument-Bromage, M.E. Warren, C.H. Borchers, and P. Tempst Histone demethylation by a family of JmjC domain-containing proteins Nature 439 2006 811 816 (Pubitemid 43255695)
189. R.J. Klose, E.M. Kallin, and Y. Zhang JmjC-domain-containing proteins and histone demethylation Nat Rev 7 2006 715 727 (Pubitemid 44260007)
190. B. Chang, Y. Chen, Y. Zhao, and R.K. Bruick JMJD6 is a histone arginine demethylase Science 318 2007 444 447 (Pubitemid 47614528)
191. J.M. Elkins, K.S. Hewitson, L.A. McNeill, J.F. Seibel, I. Schlemminger, and C.W. Pugh Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 alpha J Biol Chem 278 2003 1802 1806 (Pubitemid 36801416)
192. C.E. Dann 3rd, R.K. Bruick, and J. Deisenhofer Structure of factor-inhibiting hypoxia-inducible factor 1: an asparaginyl hydroxylase involved in the hypoxic response pathway Proc Natl Acad Sci USA 99 2002 15351 15356 (Pubitemid 35403938)
193. S. Krishnan, S. Horowitz, and R.C. Trievel Structure and function of histone h3 lysine 9 methyltransferases and demethylases Chembiochem 12 2011 254 263
194. D.J. Seward, G. Cubberley, S. Kim, M. Schonewald, L. Zhang, and B. Tripet Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins Nat Struct Mol Biol 14 2007 240 242 (Pubitemid 46355570)
195. J. Secombe, L. Li, L. Carlos, and R.N. Eisenman The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth Genes Dev 21 2007 537 551 (Pubitemid 46409469)
196. S. Iwase, F. Lan, P. Bayliss, L. de la Torre-Ubieta, M. Huarte, and H.H. Qi The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases Cell 128 2007 1077 1088 (Pubitemid 46437259)
197. J.C. Eissenberg, M.G. Lee, J. Schneider, A. Ilvarsonn, R. Shiekhattar, and A. Shilatifard The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase Nat Struct Mol Biol 14 2007 344 346 (Pubitemid 46608342)
198. M. Tahiliani, P. Mei, R. Fang, T. Leonor, M. Rutenberg, and F. Shimizu The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation Nature 447 2007 601 605 (Pubitemid 46868038)
199. J. Secombe, and R.N. Eisenman The function and regulation of the JARID1 family of histone H3 lysine 4 demethylases: the Myc connection Cell Cycle 6 2007 1324 1328 (Pubitemid 47327965)
200. L. Di Stefano, J.A. Walker, G. Burgio, D.F. Corona, P. Mulligan, and A.M. Naar Functional antagonism between histone H3K4 demethylases in vivo Genes Dev 25 2011 17 28
201. A. Yokoyama, Y. Okuno, T. Chikanishi, W. Hashiba, H. Sekine, and R. Fujiki KIAA1718 is a histone demethylase that erases repressive histone methyl marks Genes Cells 15 2010 867 873
202. Z. Liu, S. Zhou, L. Liao, X. Chen, M. Meistrich, and J. Xu Jmjd1a demethylase-regulated histone modification is essential for cAMP-response element modulator-regulated gene expression and spermatogenesis J Biol Chem 285 2010 2758 2770
203. F. Laumonnier, S. Holbert, N. Ronce, F. Faravelli, S. Lenzner, and C.E. Schwartz Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate J Med Genet 42 2005 780 786 (Pubitemid 41475255)
204. M.G. Lee, R. Villa, P. Trojer, J. Norman, K.P. Yan, and D. Reinberg Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination Science 318 2007 447 450 (Pubitemid 47614529)
205. K. Agger, P.A. Cloos, J. Christensen, D. Pasini, S. Rose, and J. Rappsilber UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development Nature 449 2007 731 734 (Pubitemid 47552088)
206. N.P. Blackledge, J.C. Zhou, M.Y. Tolstorukov, A.M. Farcas, P.J. Park, and R.J. Klose CpG islands recruit a histone H3 lysine 36 demethylase Mol Cell 38 2010 179 190
207. D.A. Hsia, C.G. Tepper, M.R. Pochampalli, E.Y. Hsia, C. Izumiya, and S.B. Huerta KDM8, a H3K36me2 histone demethylase that acts in the cyclin A1 coding region to regulate cancer cell proliferation Proc Natl Acad Sci USA 107 2010 9671 9676
208. T. Suganuma, and J.L. Workman Features of the PHF8/KIAA1718 histone demethylase Cell Res 20 2010 861 862
209. K.M. Sinha, H. Yasuda, M.M. Coombes, S.Y. Dent, and B. de Crombrugghe Regulation of the osteoblast-specific transcription factor Osterix by NO66, a Jumonji family histone demethylase Embo J 29 2010 68 79
210. M. Okamoto, M. Van Stry, L. Chung, M. Koyanagi, X. Sun, and Y. Suzuki Mina, an Il4 repressor, controls T helper type 2 bias Nat Immunol 10 2009 872 879
211. J. Eilbracht, M. Reichenzeller, M. Hergt, M. Schnolzer, H. Heid, and M. Stohr NO66, a highly conserved dual location protein in the nucleolus and in a special type of synchronously replicating chromatin Mol Biol Cell 15 2004 1816 1832 (Pubitemid 38401830)
212. Z. Chen, J. Zang, J. Whetstine, X. Hong, F. Davrazou, and T.G. Kutateladze Structural insights into histone demethylation by JMJD2 family members Cell 125 2006 691 702
213. S. Maurer-Stroh, N.J. Dickens, L. Hughes-Davies, T. Kouzarides, F. Eisenhaber, and C.P. Ponting The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains Trends Biochem Sci 28 2003 69 74 (Pubitemid 36165134)
214. A. Norris, and J.D. Boeke Silent information regulator 3: the Goldilocks of the silencing complex Genes Dev 24 2010 115 122
215. Y. Wang, B. Reddy, J. Thompson, H. Wang, K. Noma, and J.R. Yates 3rd Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein Mol Cell 33 2009 428 437
216. A. Sathyamurthy, M.D. Allen, A.G. Murzin, and M. Bycroft Crystal structure of the malignant brain tumor (MBT) repeats in Sex Comb on Midleg-like 2 (SCML2) J Biol Chem 278 2003 46968 46973 (Pubitemid 37452279)
217. N. Lancelot, G. Charier, J. Couprie, I. Duband-Goulet, B. Alpha-Bazin, and E. Quemeneur The checkpoint Saccharomyces cerevisiae Rad9 protein contains a tandem tudor domain that recognizes DNA Nucleic Acids Res 35 2007 5898 5912 (Pubitemid 47506304)
218. Y. Huyen, O. Zgheib, R.A. Ditullio Jr., V.G. Gorgoulis, P. Zacharatos, and T.J. Petty Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks Nature 432 2004 406 411 (Pubitemid 39551676)
219. I. Callebaut, and J.P. Mornon The human EBNA-2 coactivator p100: multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development Biochem J 321 Pt 1 1997 125 132 (Pubitemid 27032578)
220. H. Shimojo, N. Sano, Y. Moriwaki, M. Okuda, M. Horikoshi, and Y. Nishimura Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain J Mol Biol 378 2008 987 1001
221. L.M. Iyer, S. Abhiman, and L. Aravind MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases Biol Direct 3 2008 8
222. S.A. Jacobs, and S. Khorasanizadeh Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail Science 295 2002 2080 2083 (Pubitemid 34229471)
223. A.G. Murzin OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences EMBO J 12 1993 861 867 (Pubitemid 23095834)
224. J.F. Flanagan, L.Z. Mi, M. Chruszcz, M. Cymborowski, K.L. Clines, and Y. Kim Double chromodomains cooperate to recognize the methylated histone H3 tail Nature 438 2005 1181 1185 (Pubitemid 41831690)
225. C. Grimm, R. Matos, N. Ly-Hartig, U. Steuerwald, D. Lindner, and V. Rybin Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt EMBO J 28 2009 1965 1977
226. Y. Huang, J. Fang, M.T. Bedford, Y. Zhang, and R.M. Xu Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A Science 312 2006 748 751
227. H. Liu, J.Y. Wang, Y. Huang, Z. Li, W. Gong, and R. Lehmann Structural basis for methylarginine-dependent recognition of Aubergine by Tudor Genes Dev 24 2010 1876 1881
228. M. Perez-Alegre, A. Dubus, and E. Fernandez REM1, a new type of long terminal repeat retrotransposon in Chlamydomonas reinhardtii Mol Cell Biol 25 2005 10628 10638 (Pubitemid 41681982)
229. C.P. Ponting, L. Aravind, J. Schultz, P. Bork, and E.V. Koonin Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer J Mol Biol 289 1999 729 745 (Pubitemid 29306646)
230. S.S. Krishna, I. Majumdar, and N.V. Grishin Structural classification of zinc fingers: survey and summary Nucleic Acids Res 31 2003 532 550 (Pubitemid 36175942)
231. L. Aravind, L.M. Iyer, and E.V. Koonin Scores of RINGS but no PHDs in ubiquitin signaling Cell Cycle 2 2003 123 126
232. S. Chakravarty, L. Zeng, and M.M. Zhou Structure and site-specific recognition of histone H3 by the PHD finger of human autoimmune regulator Structure 17 2009 670 679
233. H. Li, S. Ilin, W. Wang, E.M. Duncan, J. Wysocka, and C.D. Allis Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF Nature 442 2006 91 95 (Pubitemid 44064215)
234. L. Zeng, Q. Zhang, S. Li, A.N. Plotnikov, M.J. Walsh, and M.M. Zhou Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b Nature 466 2010 258 262
235. T.C. Miller, T.J. Rutherford, C.M. Johnson, M. Fiedler, and M. Bienz Allosteric remodelling of the histone H3 binding pocket in the Pygo2 PHD finger triggered by its binding to the B9L/BCL9 co-factor J Mol Biol 401 2010 969 984
236. H. van Ingen, F.M. van Schaik, H. Wienk, J. Ballering, H. Rehmann, and A.C. Dechesne Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3 Structure 16 2008 1245 1256
237. F. He, T. Umehara, K. Saito, T. Harada, S. Watanabe, and T. Yabuki Structural insight into the zinc finger CW domain as a histone modification reader Structure 18 2010 1127 1139
238. J. Wysocka, T. Swigut, T.A. Milne, Y. Dou, X. Zhang, and A.L. Burlingame WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development Cell 121 2005 859 872 (Pubitemid 40806418)
239. A. Schuetz, A. Allali-Hassani, F. Martin, P. Loppnau, M. Vedadi, and A. Bochkarev Structural basis for molecular recognition and presentation of histone H3 by WDR5 EMBO J 25 2006 4245 4252 (Pubitemid 44435222)
240. J.F. Couture, E. Collazo, and R.C. Trievel Molecular recognition of histone H3 by the WD40 protein WDR5 Nat Struct Mol Biol 13 2006 698 703 (Pubitemid 44175162)
241. A.J. Ruthenburg, W. Wang, D.M. Graybosch, H. Li, C.D. Allis, and D.J. Patel Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Nat Struct Mol Biol 13 2006 704 712 (Pubitemid 44175163)
242. R.C. Trievel, and A. Shilatifard WDR5, a complexed protein Nat Struct Mol Biol 16 2009 678 680
243. F. Tie, C.A. Stratton, R.L. Kurzhals, and P.J. Harte The N terminus of Drosophila ESC binds directly to histone H3 and is required for E(Z)-dependent trimethylation of H3 lysine 27 Mol Cell Biol 27 2007 2014 2026 (Pubitemid 46418460)
244. R. Collins, and X. Cheng A case study in cross-talk: the histone lysine methyltransferases G9a and GLP Nucleic Acids Res 38 2010 3503 3511
245. T. Gao, R.E. Collins, J.R. Horton, X. Zhang, R. Zhang, and A. Dhayalan The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding Proteins 76 2009 772 777
246. S. Balaji, L.M. Iyer, and L. Aravind HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes Mol Biosyst 5 2009 269 275
247. M.M. Garcia-Alai, M.D. Allen, A.C. Joerger, and M. Bycroft The structure of the FYR domain of transforming growth factor beta regulator 1 Protein Sci 19 2010 1432 1438
248. A.E. Elia, P. Rellos, L.F. Haire, J.W. Chao, F.J. Ivins, and K. Hoepker The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain Cell 115 2003 83 95 (Pubitemid 37255320)
249. J. Min, X. Zhang, X. Cheng, S.I. Grewal, and R.M. Xu Structure of the SET domain histone lysine methyltransferase Clr4 Nat Struct Biol 9 2002 828 832 (Pubitemid 35257782)
250. K. Brzeska, J. Brzeski, J. Smith, and V.L. Chandler Transgenic expression of CBBP, a CXC domain protein, establishes paramutation in maize Proc Natl Acad Sci USA 107 2010 5516 5521
251. T. Fauth, F. Muller-Planitz, C. Konig, T. Straub, and P.B. Becker The DNA binding CXC domain of MSL2 is required for faithful targeting the Dosage Compensation Complex to the X chromosome Nucleic Acids Res 38 2010 3209 3221
252. S.U. Andersen, R.G. Algreen-Petersen, M. Hoedl, A. Jurkiewicz, C. Cvitanich, and U. Braunschweig The conserved cysteine-rich domain of a tesmin/TSO1-like protein binds zinc in vitro and TSO1 is required for both male and female fertility in Arabidopsis thaliana J Exp Bot 58 2007 3657 3670 (Pubitemid 350233000)
253. W.A. Krajewski, T. Nakamura, A. Mazo, and E. Canaani A motif within SET-domain proteins binds single-stranded nucleic acids and transcribed and supercoiled DNAs and can interfere with assembly of nucleosomes Mol Cell Biol 25 2005 1891 1899 (Pubitemid 40280152)
254. E. Vojnic, B. Simon, B.D. Strahl, M. Sattler, and P. Cramer Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription J Biol Chem 281 2006 13 15 (Pubitemid 43671156)
255. K.O. Kizer, H.P. Phatnani, Y. Shibata, H. Hall, A.L. Greenleaf, and B.D. Strahl A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation Mol Cell Biol 25 2005 3305 3316 (Pubitemid 40464330)
256. R. Kanagaraj, D. Huehn, A. MacKellar, M. Menigatti, L. Zheng, and V. Urban RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription Nucleic Acids Res 38 2010 8131 8140
257. M.N. Islam, D. Fox 3rd, R. Guo, T. Enomoto, and W. Wang RecQL5 promotes genome stabilization through two parallel mechanismsinteracting with RNA polymerase II and acting as a helicase Mol Cell Biol 30 2010 2460 2472
258. R.J. Ingham, K. Colwill, C. Howard, S. Dettwiler, C.S. Lim, and J. Yu WW domains provide a platform for the assembly of multiprotein networks Mol Cell Biol 25 2005 7092 7106 (Pubitemid 41105907)
259. L.M. Iyer, E.V. Koonin, and L. Aravind Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases BMC Struct Biol 3 2003 1
260. S.A. Muljo, C. Kanellopoulou, and L. Aravind MicroRNA targeting in mammalian genomes: genes and mechanisms Wiley Interdiscip Rev Syst Biol Med 2 2010 148 161
261. S.A. Juranek, S. Rupprecht, J. Postberg, and H.J. Lipps snRNA and heterochromatin formation are involved in DNA excision during macronuclear development in stichotrichous ciliates Eukaryot Cell 4 2005 1934 1941 (Pubitemid 41636885)
262. Y. Liu, S.D. Taverna, T.L. Muratore, J. Shabanowitz, D.F. Hunt, and C.D. Allis RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena Genes Dev 21 2007 1530 1545 (Pubitemid 46955725)
263. E.L. Gerace, M. Halic, and D. Moazed The methyltransferase activity of Clr4Suv39h triggers RNAi independently of histone H3K9 methylation Mol Cell 39 2010 360 372
264. S. Feng, S.J. Cokus, X. Zhang, P.Y. Chen, M. Bostick, and M.G. Goll Conservation and divergence of methylation patterning in plants and animals Proc Natl Acad Sci USA 107 2010 8689 8694
265. A. Zemach, I.E. McDaniel, P. Silva, and D. Zilberman Genome-wide evolutionary analysis of eukaryotic DNA methylation Science 328 2010 916 919
266. J. Wang, S. Hevi, J.K. Kurash, H. Lei, F. Gay, and J. Bajko The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation Nat Genet 41 2009 125 129
267. C. Choudhary, C. Kumar, F. Gnad, M.L. Nielsen, M. Rehman, and T.C. Walther Lysine acetylation targets protein complexes and co-regulates major cellular functions Science 325 2009 834 840