Structural Biology of Epigenetic Targets

Epigenetic Targets in Drug Discovery

Volumn 42, Issue , 2010, Pages 23-56

  Romier, Christophe ^a   Wurtz, Jean Marie ^a   Renaud, Jean Paul ^a   Cavarelli, Jean ^a  

^a INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Epigenetics; Histone modifying enzymes; Structural knowledge

Indexed keywords

EID: 85018193734     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527627073.ch2     Document Type: Chapter

References (124)

1. Li, B., Carey, M. and Workman, J.L. (2007) The role of chromatin during transcription. Cell, 128(4), 707-719.
2. Groth, A., Rocha, W., Verreault, A. and Almouzni, G. (2007) Chromatin challenges during DNA replication and repair. Cell, 128(4), 721-733.
3. Feinberg, A.P. (2007) Phenotypic plasticity and the epigenetics of human disease. Nature, 447 (7143), 433-440.
4. Wang, G.G., Allis, C.D. and Chi, P. (2007) Chromatin remodeling and cancer. Part II: ATP-dependent chromatin remodeling. Trends in Molecular Medicine, 13(9), 373-380.
5. Wang, G.G., Allis, C.D. and Chi, P. (2007) Chromatin remodeling and cancer. Part I: Covalent histone modifications. Trends in Molecular Medicine, 13(9), 363-372.
6. Kouzarides, T. (2007) Chromatin modifications and their function. Cell, 128(4), 693-705.
7. Strahl, B.D. (2000) Allis CD: The language ofcovalent histone modifications. Nature, 403(6765), 41-45.
8. Jenuwein, T. and Allis, C.D. (2001) Translating the histone code. Science, 293 (5532), 1074-1080.
9. Yang, X.J. and Seto, E. (2007) HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention. Oncogene, 26(37), 5310-5318.
10. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. and Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature, 389(6648), 251-260.
11. Taverna, S.D., Li, H., Ruthenburg, A.J., Allis, C.D. and Patel, D.J. (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nature Structural & Molecular Biology, 14(11), 1025-1040.
12. Lee, K.K. and Workman, J.L. (2007) Histone acetyltransferase complexes:one size doesn't fit all. Nature Reviews. Molecular Cell Biology, 8 (4), 284-295.
13. Yang, X.J. and Seto, E. (2008) Lysine acetylation: codified crosstalk with other posttranslational modifications. Molecular Cell, 31(4), 449-461.
14. Neuwald, A.F. and Landsman, D. (1997) GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends in Biochemical Sciences, 22(5), 154-155.
15. Angus-Hill, M.L., Dutnall, R.N., Tafrov, S.T., Sternglanz, R. and Ramakrishnan, V. (1999) Crystal structure of the histone acetyltransferase Hpa2: A tetrameric member of the Gcn5-related N-acetyltransferase superfamily. Journal of Molecular Biology, 294(5), 1311-1325.
16. Dutnall, R.N., Tafrov, S.T., Sternglanz, R. and Ramakrishnan, V. (1998) Structure of the histone acetyltransferase Hat1: a paradigm for the GCN5-related N-acetyltransferase superfamily. Cell, 94(4), 427-438.
17. Rojas, J.R., Trievel, R.C., Zhou, J., Mo, Y., Li, X., Berger, S.L., Allis, C.D. and Marmorstein, R. (1999) Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide. Nature, 401(6748), 93-98.
18. Lin, Y., Fletcher, C.M., Zhou, J., Allis, C.D. and Wagner, G. (1999) Solution structure of the catalytic domain of GCN5 histone acetyltransferase bound to coenzyme A. Nature, 400(6739), 86-89.
19. Clements, A., Rojas, J.R., Trievel, R.C., Wang, L., Berger, S.L. and Marmorstein, R. (1999) Crystal structure of the histone acetyltransferase domain of the human PCAF transcriptional regulator bound to coenzyme A. The EMBO Journal, 18(13), 3521-3532.
20. Dutnall, R.N., Tafrov, S.T., Sternglanz, R. and Ramakrishnan, V. (1998) Structure of the yeast histone acetyltransferase Hat1: insights into substrate specificity and implications for the Gcn5-related N-acetyltransferase superfamily. Cold Spring Harbor Symposia on Quantitative Biology, 63, 501-507.
21. Trievel, R.C., Rojas, J.R., Sterner, D.E., Venkataramani, R.N., Wang, L., Zhou, J., Allis, C.D., Berger, S.L. and Marmorstein, R. (1999) Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator. Proceedings of the National Academy of Sciences ofthe United States ofAmerica, 96(16), 8931-8936.
22. Yan, Y., Barlev, N.A., Haley, R.H., Berger, S. L. and Marmorstein, R. (2000) Crystal structure of yeast Esa1 suggests a unified mechanism for catalysis and substrate binding by histone acetyltransferases. Molecular Cell, 6(5), 1195-1205.
23. Holbert, M.A., Sikorski, T., Carten, J., Snowflack, D., Hodawadekar, S. and Marmorstein, R. (2007) The human monocytic leukemia zinc finger histone acetyltransferase domain contains DNA-binding activity implicated in chromatin targeting. The Journal of Biological Chemistry, 282(50), 36603-36613.
24. Liu, X., Wang, L., Zhao, K., Thompson, P.R., Hwang, Y., Marmorstein, R. and Cole, P.A. (2008) The structural basis of protein acetylation by the p300/CBP transcriptional coactivator. Nature, 451(7180), 846-850.
25. Lin, C. and Yuan, Y.A. (2008) Structural insights into histone H3 lysine 56 acetylation by Rtt109. Structure, 16(10), 1503-1510.
26. Stavropoulos, P., Nagy, V., Blobel, G. and Hoelz, A. (2008) Molecular basis for the autoregulation of the protein acetyl transferase Rtt109. Proceedings ofthe National Academy of Sciences of the United States of America, 105(34), 12236-12241.
27. Tang, Y., Holbert, M.A., Wurtele, H., Meeth, K., Rocha, W., Gharib, M., Jiang, E., Thibault, P., Verrault, A., Cole, P.A. et al. (2008) Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP. Nature Structural & Molecular Biology, 15(7), 738-745.
28. Poux, A.N. and Marmorstein, R. (2003) Molecular basis for Gcn5/PCAF histone acetyltransferase selectivity for histone and nonhistone substrates. Biochemistry, 42(49), 14366-14374.
29. Poux, A.N., Cebrat, M., Kim, C.M., Cole, P.A. and Marmorstein, R. (2002) Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor. Proceedings ofthe National Academy of Sciences of the United States of America, 99(22), 14065-14070.
30. Clements, A., Poux, A.N., Lo, W.S., Pillus, L., Berger, S.L. and Marmorstein, R. (2003) Structural basis for histone and phosphohistone binding by the GCN5 histone acetyltransferase. Molecular Cell, 12(2), 461-473.
31. Tanner, K.G., Trievel, R.C., Kuo, M.H., Howard, R.M., Berger, S.L., Allis, C.D., Marmorstein, R. and Denu, J.M. (1999) Catalytic mechanism and function of invariant glutamic acid 173 from the histone acetyltransferase GCN5 transcriptional coactivator. The Journal of Biological Chemistry, 274(26), 18157-18160.
32. Yan, Y., Harper, S., Speicher, D.W. and Marmorstein, R. (2002) The catalytic mechanism of the ESA1 histone acetyltransferase involves a self-acetylated intermediate. Nature Structural Biology, 9(11), 862-869.
33. Berndsen, C.E., Albaugh, B.N., Tan, S. and Denu, J.M. (2007) Catalytic mechanism of a MYST family histone acetyltransferase. Biochemistry, 46(3), 623-629.
34. Yang, X.J. and Seto, E. (2003) Collaborative spirit of histone deacetylases in regulating chromatin structure and gene expression. Current Opinion in Genetics & Development, 13(2), 143-153.
35. Glozak, M.A., Sengupta, N., Zhang, X. and Seto, E. (2005) Acetylation and deacetylation of non-histone proteins. Gene, 363, 15-23.
36. Gregoretti, I.V., Lee, Y.M. and Goodson, H.V. (2004) Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis. Journal of Molecular Biology, 338(1), 17-31.
37. de Ruijter, A.J., van Gennip, A.H., Caron, H.N., Kemp, S. and van Kuilenburg, A.B. (2003) Histone deacetylases (HDACs): characterization of the classical HDAC family. The Biochemical Journal, 370 (Pt 3), 737-749.
38. Leipe, D.D. and Landsman, D. (1997) Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily. Nucleic Acids Research, 25(18), 3693-3697.
39. Yang, X.J. and Seto, E. (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nature Reviews. Molecular Cell Biology, 9(3), 206-218.
40. Fischle, W., Dequiedt, F., Hendzel, M.J., Guenther, M.G., Lazar, M.A., Voelter, W. and Verdin, E. (2002) Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR. Molecular Cell, 9(1), 45-57.
41. Finnin, M.S., Donigian, J.R., Cohen, A., Richon, V.M., Rifkind, R.A., Marks, P.A., Breslow, R. and Pavletich, N.P. (1999) Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature, 401(6749), 188-193.
42. Somoza, J.R., Skene, R.J., Katz, B.A., Mol, C., Ho, J.D., Jennings, A.J., Luong, C., Arvai, A., Buggy, J.J., Chi, E. et al. (2004) Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure (London, England: 1993), 12(7), 1325-1334.
43. Vannini, A., Volpari, C., Filocamo, G., Casavola, E.C., Brunetti, M., Renzoni, D., Chakravarty, P., Paolini, C., De Francesco, R., Gallinari, P. et al. (2004) Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor. Proceedings of the National Academy ofSciences ofthe United States of America, 101 (42), 15064-15069.
44. Nielsen, T.K., Hildmann, C., Dickmanns, A., Schwienhorst, A. and Ficner, R. (2005) Crystal structure of a bacterial class 2 histone deacetylase homologue. Journal of Molecular Biology, 354(1), 107-120.
45. Schuetz, A., Min, J., Allali-Hassani, A., Schapira, M., Shuen, M., Loppnau, P., Mazitschek, R., Kwiatkowski, N.P., Lewis, T.A., Maglathin, R.L. et al. (2008) Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity. The Journal ofBiological Chemistry, 283(17), 11355-11363.
46. Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C. et al. (2008) Structural and functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zinc-binding domain. The Journal ofBiological Chemistry, 283(39), 26694-26704.
47. Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfi, A., De Francesco, R., Steinkuhler, C. and Di Marco, S. (2007) Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex. EMBO Reports, 8(9), 879-884.
48. Nielsen, S.J., Schneider, R., Bauer, U.M., Bannister, A.J., Morrison, A., O'Carroll, D., Firestein, R., Cleary, M., Jenuwein, T., Herrera, R.E. et al. (2001) Rb targets histone H3 methylation and HP1 to promoters. Nature, 412(6846), 561-565.
49. Vanommeslaeghe, K., De Proft, F., Loverix, S., Tourwe, D. and Geerlings, P. (2005) Theoretical study revealing the functioning of a novel combination of catalytic motifs in histone deacetylase. Bioorganic and Medicinal Chemistry, 13(12), 3987-3992.
50. Lahm, A., Paolini, C., Pallaoro, M., Nardi, M.C., Jones, P., Neddermann, P., Sambucini, S., Bottomley, M.J., Lo Surdo, P., Carfi, A. et al. (2007) Unraveling the hidden catalytic activity of vertebrate class IIa histone deacetylases. Proceedings of the National Academy of Sciences of the United States of America, 104(44), 17335-17340.
51. Hodawadekar, S.C. and Marmorstein, R. (2007) Chemistry of acetyl transfer by histone modifying enzymes: structure, mechanism and implications for effector design. Oncogene, 26(37), 5528-5540.
52. Sauve, A.A., Wolberger, C., Schramm, V.L. and Boeke, J.D. (2006) The biochemistry ofsirtuins. AnnualReview of Biochemistry, 75, 435-465.
53. Finnin, M.S., Donigian, J.R. and Pavletich, N.P. (2001) Structure of the histone deacetylase SIRT2. Nature Structural Biology, 8(7), 621-625.
54. Min, J., Landry, J., Sternglanz, R. and Xu, R.M. (2001) Crystal structure of a SIR2 homolog-NAD complex. Cell, 105(2), 269-279.
55. Chang, J.H., Kim, H.C., Hwang, K.Y., Lee, J.W., Jackson, S.P., Bell, S.D. and Cho, Y. (2002) Structural basis for the NAD-dependent deacetylase mechanism of Sir2. The Journal ofBiological Chemistry, 277(37), 34489-34498.
56. Zhao, K., Harshaw, R., Chai, X. and Marmorstein, R. (2004) Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD( + )-dependent Sir2 histone/protein deacetylases. Proceedings of the National Academy of Sciences of the United States of America, 101(23), 8563-8568.
57. Avalos, J.L., Boeke, J.D. and Wolberger, C. (2004) Structural basis for the mechanism and regulation ofSir2 enzymes. Molecular Cell, 13(5), 639-648.
58. Zhao, K., Chai, X. and Marmorstein, R. (2003) Structure ofthe yeast Hst2 protein deacetylase in ternary complex with 20-O-acetyl ADP ribose and histone peptide. Structure (London, England: 1993), 11(11), 1403-1411.
59. Avalos, J.L., Celic, I., Muhammad, S., Cosgrove, M.S., Boeke, J.D. and Wolberger, C. (2002) Structure of a Sir2 enzyme bound to an acetylated p53 peptide. Molecular Cell, 10(3), 523-535.
60. Hoff, K.G., Avalos, J.L., Sens, K. and Wolberger, C. (2006) Insights into the sirtuin mechanism from ternary complexes containing NAD + and acetylated peptide. Structure (London, England: 1993), 14(8), 1231-1240.
61. Cosgrove, M.S., Bever, K., Avalos, J.L., Muhammad, S., Zhang, X. and Wolberger, C. (2006) The structural basis of sirtuin substrate affinity. Biochemistry, 45(24), 7511-7521.
62. Bitterman, K.J., Anderson, R.M., Cohen, H.Y., Latorre-Esteves, M. and Sinclair, D.A. (2002) Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast sir2 and human SIRT1. The Journal of Biological Chemistry, 277(47), 45099-45107.
63. Sanders, B.D., Zhao, K., Slama, J.T. and Marmorstein, R. (2007) Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes. Molecular Cell, 25(3), 463-472.
64. Avalos, J.L., Bever, K.M. and Wolberger, C. (2005) Mechanism of sirtuin inhibition by nicotinamide: altering the NAD( +) cosubstrate specificity of a Sir2 enzyme. Molecular Cell, 17(6), 855-868.
65. Cheng, X., Collins, R.E. and Zhang, X. (2005) Structural and sequence motifs of protein (histone) methylation enzymes. Annual Review ofBiophysics and Biomolecular Structure, 34, 267-294.
66. Lee, D.Y., Teyssier, C., Strahl, B.D. and Stallcup, M.R. (2005) Role of protein methylation in regulation of transcription. Endocrine Reviews, 26(2), 147-170.
67. Polevoda, B. and Sherman, F. (2007) Methylation of proteins involved in translation. MolecularMicrobiology, 65(3), 590-606.
68. Kozbial, P.Z. and Mushegian, A.R. (2005) Natural history of S-adenosylmethionine-binding proteins. BMC Structural Biology, 5, 19.
69. Schubert, H.L., Blumenthal, R.M. and Cheng, X. (2003) Many paths to methyltransfer: a chronicle of convergence. Trends in Biochemical Sciences, 28(6), 329-335.
70. Cheng, X. and Zhang, X. (2007) Structural dynamics of protein lysine methylation and demethylation. Mutation Research, 618 (1-2), 102-115.
71. Baumbusch, L.O., Thorstensen, T., Krauss, V., Fischer, A., Naumann, K., Assalkhou, R., Schulz, I., Reuter, G. and Aalen, R.B. (2001) The Arabidopsis thaliana genome contains at least 29 active genes encoding SETdomain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Research, 29 (21), 4319-4333.
72. Kouzarides, T. (2002) Histone methylation in transcriptional control. Current Opinion in Genetics & Development, 12(2), 198-209.
73. Rea, S., Eisenhaber, F., O'Carroll, D., Strahl, B.D., Sun, Z.W., Schmid, M., Opravil, S., Mechtler, K., Ponting, C.P., Allis, C.D. et al. (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature, 406(6796), 593-599.
74. Qian, C. and Zhou, M.M. (2006) SET domain protein lysine methyltransferases: Structure, specificity and catalysis. Cellular and Molecular Life Sciences, 63(23), 2755-2763.
75. Dillon, S.C., Zhang, X., Trievel, R.C. and Cheng, X. (2005) The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biology, 6(8), 227.
76. Smith, B.C. and Denu, J.M. (Jun 14 2008) Chemical mechanisms of histone lysine and arginine modifications. Biochimica et Biophysica Acta (Epub ahead of print).
77. Singer, M.S., Kahana, A., Wolf, A.J., Meisinger, L.L., Peterson, S.E., Goggin, C., Mahowald, M. and Gottschling, D.E. (1998) Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics, 150(2), 613-632.
78. Min, J., Feng, Q., Li, Z., Zhang, Y. andXu, R.M. (2003) Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell, 112(5), 711-723.
79. Sawada, K., Yang, Z., Horton, J.R., Collins, R.E., Zhang, X. and Cheng, X. (2004) Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase. The Journal of Biological Chemistry, 279(41), 43296-43306.
80. Pahlich, S., Zakaryan, R.P. and Gehring, H. (2006) Protein arginine methylation: Cellular functions and methods of analysis. Biochimica et Biophysica Acta, 1764(12), 1890-1903.
81. Krause, C.D., Yang, Z.H., Kim, Y.S., Lee, J.H., Cook, J.R. and Pestka, S. (2007) Protein arginine methyltransferases: Evolution and assessment of their pharmacological and therapeutic potential. Pharmacology & Therapeutics, 113(1), 50-87.
82. Bedford, M.T. (2007) Arginine methylation at a glance. Journal of Cell Science, 120 (Pt 24), 4243-4246.
83. Zhang, X. and Cheng, X. (2003) Structure of the Predominant Protein Arginine Methyltransferase PRMT1 and Analysis of Its Binding to Substrate Peptides. Structure (Camb), 11(5), 509-520.
84. Zhang, X., Zhou, L. and Cheng, X. (2000) Crystal structure ofthe conserved core of protein arginine methyltransferase PRMT3. The EMBO Journal, 19(14), 3509-3519.
85. Weiss, V.H., McBride, A.E., Soriano, M.A., Filman, D.J., Silver, P.A. and Hogle, J.M. (2000) The structure and oligomerization of the yeast arginine methyltransferase, Hmt1. Nature Structural Biology, 7(12), 1165-1171.
86. Yue, W.W., Hassler, M., Roe, S.M., Thompson-Vale, V. and Pearl, L.H. (2007) Insights into histone code syntax from structural and biochemical studies of CARM1 methyltransferase. The EMBO Journal, 26(20), 4402-4412.
87. Troffer-Charlier, N., Cura, V., Hassenboehler, P., Moras, D. and Cavarelli, J. (2007) Functional insights from structures ofcoactivator-associated arginine methyltransferase 1 domains. The EMBOJournal, 26 (20), 4391-4401.
88. Martin, J.L. and McMillan, F.M. (2002) SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Current Opinion in Structural Biology, 12(6), 783-793.
89. Anand, R. and Marmorstein, R. (2007) Structure and mechanism of lysine-specific demethylase enzymes. The Journal of Biological Chemistry, 282(49), 35425-35429.
90. Shi, Y. and Whetstine, J.R. (2007) Dynamic regulation of histone lysine methylation by demethylases. Molecular Cell, 25(1), 1-14.
91. Klose, R.J. and Zhang, Y. (2007) Regulation of histone methylation by demethylimination and demethylation. Nature Reviews. Molecular Cell Biology, 8(4), 307-318.
92. Wang, Y., Wysocka, J., Sayegh, J., Lee, Y.H., Perlin, J.R., Leonelli, L., Sonbuchner, L.S., McDonald, C.H., Cook, R.G., Dou, Y. et al. (2004) Human PAD4 regulates histone arginine methylation levels via demethylimination. Science, 306(5694), 279-283.
93. Thompson, P.R. and Fast, W. (2006) Histone citrullination by protein arginine deiminase: is arginine methylation a green light or a roadblock? ACS Chemical Biology, 1(7), 433-441.
94. Chang, B., Chen, Y., Zhao, Y. and Bruick, R.K. (2007) JMJD6 is a histone arginine demethylase. Science, 318(5849), 444-447.
95. Lan, F., Nottke, A.C. and Shi, Y. (2008) Mechanisms involved in the regulation of histone lysine demethylases. Current Opinion in Cell Biology, 20(3), 316-325.
96. Trewick, S.C., McLaughlin, P.J. and Allshire, R.C. (2005) Methylation: lost in hydroxylation? EMBO Reports, 6(4), 315-320.
97. Tsukada, Y., Fang, J., Erdjument-Bromage, H., Warren, M.E., Borchers, C.H., Tempst, P. and Zhang, Y. (2006) Histone demethylation by a family of JmjC domain-containing proteins. Nature, 439(7078), 811-816.
98. Chen, Y., Yang, Y., Wang, F., Wan, K., Yamane, K., Zhang, Y. and Lei, M. (2006) Crystal structure ofhumanhistone lysine-specific demethylase 1 (LSD1). Proceedings of the National Academy of Sciences ofthe United States ofAmerica, 103(38), 13956-13961.
99. Stavropoulos, P., Blobel, G. and Hoelz, A. (2006) Crystal structure and mechanism of human lysine-specific demethylase-1. Nature Structural & Molecular Biology, 13(7), 626-632.
100. Mimasu, S., Sengoku, T., Fukuzawa, S., Umehara, T. and Yokoyama, S. (2008) Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A. Biochemical and Biophysical Research Communications, 366(1), 15-22.
101. Lee, M.G., Wynder, C., Cooch, N. and Shiekhattar, R. (2005) An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature, 437(7057), 432-435.
102. Shi, Y.J., Matson, C., Lan, F., Iwase, S., Baba, T. and Shi, Y. (2005) Regulation of LSD1 histone demethylase activity by its associated factors. Molecular Cell, 19(6), 857-864.
103. Yang, M., Gocke, C.B., Luo, X., Borek, D., Tomchick, D.R., Machius, M., Otwinowski, Z. and Yu, H. (2006) Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Molecular Cell, 23(3), 377-387.
104. Forneris, F., Binda, C., Adamo, A., Battaglioli, E. and Mattevi, A. (2007) Structural basis of LSD1-CoREST selectivity in histone H3 recognition. The Journal of Biological Chemistry, 282(28), 20070-20074.
105. Yang, M., Culhane, J.C., Szewczuk, L.M., Gocke, C.B., Brautigam, C.A., Tomchick, D.R., Machius, M., Cole, P.A. and Yu, H. (2007) Structural basis of histone demethylation by LSD1 revealed by suicide inactivation. Nature Structural & Molecular Biology, 14(6), 535-539.
106. Yang, M., Culhane, J.C., Szewczuk, L.M., Jalili, P., Ball, H.L., Machius, M., Cole, P.A. and Yu, H. (2007) Structural basis for the inhibition of the LSD1 histone demethylase bythe antidepressanttrans-2-phenylcyclopropylamine. Biochemistry, 46(27), 8058-8065.
107. Chen, Z., Zang, J., Whetstine, J., Hong, X., Davrazou, F., Kutateladze, T.G., Simpson, M., Mao, Q., Pan, C.H., Dai, S. et al. (2006) Structural insights into histone demethylation by JMJD2 family members. Cell, 125(4), 691-702.
108. Chen, Z., Zang, J., Kappler, J., Hong, X., Crawford, F., Wang, Q., Lan, F., Jiang, C., Whetstine, J., Dai, S. et al. (2007) Structural basis of the recognition of a methylated histone tail by JMJD2A. Proceedings of the National Academy of Sciences of the United States of America, 104(26), 10818-10823.
109. Ng, S.S., Kavanagh, K.L., McDonough, M.A., Butler, D., Pilka, E.S., Lienard, B.M., Bray, J.E., Savitsky, P., Gileadi, O., von Delft, F. et al. (2007) Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature, 448(7149), 87-91.
110. Cuthbert, G.L., Daujat, S., Snowden, A.W., Erdjument-Bromage, H., Hagiwara, T., Yamada, M., Schneider, R., Gregory, P.D., Tempst, P., Bannister, A.J. et al. (2004) Histone deimination antagonizes arginine methylation. Cell, 118(5), 545-553.
111. Arita, K., Hashimoto, H., Shimizu, T., Nakashima, K., Yamada, M. and Sato, M. (2004) Structural basis for Ca(2 +)-induced activation of human PAD4. Nature Structural & Molecular Biology, 11(8), 777-783.
112. Arita, K., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M. and Sato, M. (2006) Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4. Proceedings of the National Academy of Sciences of the United States of America, 103(14), 5291-5296.
113. Goll, M.G. and Bestor, T.H. (2005) Eukaryotic cytosine methyltransferases. Annual Review of Biochemistry, 74, 481-514.
114. Cheng, X. and Blumenthal, R.M. (2008) Mammalian DNA methyltransferases:a structural perspective. Structure (London, England: 1993), 16(3), 341-350.
115. Jia, D., Jurkowska, R.Z., Zhang, X., Jeltsch, A. and Cheng, X. (2007) Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature, 449(7159), 248-251.
116. Ooi, S.K., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument-Bromage, H., Tempst, P., Lin, S.P., Allis, C.D. et al. (2007) DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature, 448(7154), 714-717.
117. Klimasauskas, S., Kumar, S., Roberts, R.J. and Cheng, X. (1994) HhaI methyltr-ansferase flips its target base out of the DNA helix. Cell, 76(2), 357-369.
118. Reinisch, K.M., Chen, L., Verdine, G.L. and Lipscomb, W.N. (1995) The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell, 82(1), 143-153.
119. O'Gara, M., Klimasauskas, S., Roberts, R.J. and Cheng, X. (1996) Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes. Journal of Molecular Biology, 261 (5), 634-645.
120. Metivier, R., Gallais, R., Tiffoche, C., Le Peron, C., Jurkowska, R.Z., Carmouche, R.P., Ibberson, D., Barath, P., Demay, F., Reid, G. et al. (2008) Cyclical DNA methylation of a transcriptionally active promoter. Nature, 452(7183), 45-50.
121. Kangaspeska, S., Stride, B., Metivier, R., Polycarpou-Schwarz, M., Ibberson, D., Carmouche, R.P., Benes, V., Gannon, F. and Reid, G. (2008) Transient cyclical methylation of promoter DNA. Nature, 452(7183), 112-115.
122. Mujtaba, S., Zeng, L. and Zhou, M.M. (2007) Structure and acetyl-lysine recognition of the bromodomain. Oncogene, 26(37), 5521-5527.
123. Perrakis, A. and Romier, C. (2008) Assembly of protein complexes by coexpression in prokaryotic and eukaryotic hosts: an overview. Methods in Molecular Biology (Clifton, NJ), 426, 247-256.
124. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M. and Seraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnology, 17(10), 1030-1032.