Cheng lab publications, sorted by date

(email xcheng@emory.edu for PDF)

2012

133. Upadhyay AK, Rotili D, Han JW, Hu R, Chang Y, Labella D, Zhang X, Yoon YS, Mai A, Cheng X. (2012) An Analog of BIX-01294 Selectively Inhibits a Family of Histone H3 Lysine 9 Jumonji Demethylases. J. Mol. Biol. 416, 319-327 [Epub Dec 29 2011] (view coverimage)

132. Nicholson TB, Su H, Hevi S, Wang J, Bajko J, Li M, Valdez R, Loureiro J, Cheng X, Li E, Kinzel B, Labow M, Chen T. (2012) Defective heart development in hypomorphic LSD1 mice. Cell Res. [Epub Dec 6 2011] doi: 10.1038/cr.2011.194.

2011

130. Szulwach KE, Li X, Li Y, Song CX, Wu H, Dai Q, Irier H, Upadhyay AK, Gearing M, Levey AI, Vasanthakumar A, Godley LA, Chang Q, Cheng X, He C, Jin P (2011) 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci. 14, 1607-16 [Epub Oct 30] • News and Views by Flax and Soloway: Methylation on the mind • Emory University News Release: Patterns of New DNA Letter in Brain Suggest Distinct Function - Vocabulary of epigenetics expanding

129. Zhao J, Du Y, Horton JR, Upadhyay AK, Lou B, Bai Y, Zhang X, Du L, Li M, Wang B, Zhang L, Barbieri JT, Khuri FR, Cheng X, Fu H (2011) Discovery and structural characterization of a small molecule 14-3-3 protein-protein interaction inhibitor. PNAS 108, 16212-6 [Epub Sept 9] • Emory University News Release: X-ray Protein Probe Leads to Potential Anticancer Tactic

128. Upadhyay AK, Horton JR, Zhang X, Cheng X (2011) Coordinated methyl-lysine erasure: structural and functional linkage of a Jumonji demethylase domain and a reader domain. Curr Opin Struct Biol. 21, 750-760 [Epub Aug 25]
 
127. Cheng X, Blumenthal RM. (2011) Epiphanies in epigenetics. Prog. Mol. Biol. Transl. Sci. 101, 1-21. (Preface for the volume - Modification of Nuclear DNA and its Regulatory Proteins, Cheng and Blumenthal, editors; ISBN 978-0-12-387685-0)

126. Chang Y, Levy D, Horton JR, Peng J, Zhang X, Gozani O, Cheng X (2011) Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling. Nucleic Acids Res. 39, 6380-6389 [Epub April 22] (view coverimage)

125. Chang Y, Horton JR, Bedford MT, Zhang X, Cheng X (2011) Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding. J. Mol. Biol. 408, 807-14 [Epub March 23]

124. Horton JR, Upadhyay AK, Hashimoto H, Zhang X, Cheng X (2011) Structural basis for human PHF2 Jumonji domain interaction with metal ions. J. Mol. Biol. 406, 1-8 [Epub 2010 Dec 15]

123. Estève PO, Chang Y, Samaranayake M, Upadhyay AK, Horton JR, Feehery GR, Cheng X, Pradhan S (2011) A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability. Nat Struct Mol Biol. 18, 42-48 [Epub 2010 Dec 12]

122. Levy D, Kuo, AJ, Chang Y, Schaefer U, Kitson C, Cheung P, Espejo A, Zee BM, Liu CL, Tangsombatvisit S, Tennen RI, Kuo AY, Tanjing S, Cheung R, Chua KF, Utz PJ, Shi X, Prinjha RK, Lee K, Garcia BA, Bedford MT, Tarakhovsky A, Cheng X, Gozani O (2011) Lysine methylation of the NF-kB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-kB signaling. Nat Immunol. 12, 29-36 [Epub 2010 Dec 5] • News and Views by Moscat and Diaz-Meco: Fine tuning NF-κB: new openings for PKC-ζ. • Research Highlight by Yang and Chen: Talking to histone: methylated RelA serves as a messenger.

121. Upadhyay AK, Cheng X (2011) Dynamics of histone lysine methylation: structures of methyl writers and erasers. Prog Drug Res 67, 107-124 (Epigenetics and Disease, S. Gasser and E. Li, editors, ISBN: 978-3-7643-8988-8)

2010

120. Hashimoto H, Vertino PM, Cheng X (2010) Molecular coupling of DNA methylation and histone methylation. Epigenomics 2, 657-669 (PDF)

119. Cheng X, Hashimoto H, Horton JR, Zhang X (2010) Mechanisms of DNA methylation, methyl-CpG recognition, and demethylation in mammals. In: Handbook of Epigenetics: The New Molecular and Medical Genetics (Trygve Tollefsbol, editor). Oxford: Academic Press (ISBN: 978-0-12-375709-8) (DOI: 10.1016/B978-0-12-375709-8.00002-2) pp 9-24 (PDF)

118. Lee CF, Ou DS, Lee SB, Chang LH, Lin RK, Li YS, Upadhyay AK, Cheng X, Wang YC, Hsu HS, Hsiao M, Wu CW, Juan LJ (2010) hNaa10p contributes to tumorigenesis by facilitating DNMT1-mediated tumor suppressor gene silencing. J Clin Invest. 120, 2920-30 [Epub July 1]

117. Chang Y, Ganesh T, Horton JR, Spannhoff A, Liu J, Sun A, Zhang X, Bedford MT, Shinkai Y, Snyder JP, Cheng X (2010) Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases. J Mol Biol. 400, 1-7 [Epub Apr 28] (view coverimage)

116. Cheng X and Blumenthal RM (2010) Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochemistry 49, 2999-3008 [Epub March 8]

115. Cheng X and Roberts RJ (2010) Base Flipping. In: ENCYCLOPEDIA OF LIFE SCIENCES, John Wiley & Sons, Ltd: Chichester http://www.els.net/ [DOI: 10.1002/9780470015902.a0002714.pub2]

114. Collins R and Cheng X (2010) A case study in cross-talk: the histone lysine methyltransferases G9a and GLP. Nucleic Acids Res. 38(11), 3503-11 [Epub February 16]

113. Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X (2010) Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol. 17, 38-43 [Epub 2009 Dec 20] • Emory University News Release: Scientists Take a Step Towards Uncovering the "Histone Code" • Emory report: Closing in on 'histone code' • F1000 evaluation • Beyond genomics: New advancecs in epigenetics research • Paying Down Darwinism's Explanatory Debt • Editors (NCB) choices from the recent literature - Epigenetics: Methylation coordination • Featured in ScienceWatch From Thomson Reuters:  Fast Break Paper Commentary

2009

112. Qian Z, Horton JR, Cheng X, Lutz S (2009) Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation. J. Mol. Biol. 393, 191-201 [Epub Aug 13]

111. Jia D, Cheng, X (2009) Methylation on the nucleosome: From DNA to histone. In Nutrients and Epigenetics (eds. Choi, Sang-Woon; Friso, Simonetta, ISBN: 9781420063547, Publication Date: May 04, 2009; 258p) pp 7-35 (view coverimage)

110. Cheng X, Blumenthal RM (2009) Structural and biochemical advances in mammalian DNA methylation. In Epigenomics (Eds. Ferguson-Smith, Anne C.; Greally, John M.; Martienssen, Rob A. 2009, XIV, 442 p. ISBN: 978-1-4020-9186-5) pp 85-100 (view coverimage)

109. Gao T, Collins RE, Horton JR, Zhang X, Zhang R, Dhayalan A, Tamas R, Jeltsch A, Cheng X (2009) The ankyrin repeat domain of huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding. Proteins 76, 772-777 [Epub Apr 8]

108. Chang Y, Zhang X, Horton JR, Upadhyay AK, Spannhoff A, Liu J, Snyder JP, Bedford MT, Cheng X (2009) Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294. Nat Struct Mol Biol. 16, 312-7 [Epub Feb 15]

107. Hashimoto H, Horton JR, Zhang X, Cheng X. (2009) UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Epigenetics 4, 8-14 [Epub Jan 10] (view coverimage)

2008

106. Cheng X, Blumenthal RM (2008) Structures and activities of mammalian DNA methyltransferases. In DNA and RNA Modification Enzymes: Comparative Structure, Mechanism, Functions, Cellular Interactions and Evolution (Edited by: Henri Grosjean, ISBN: 978-1-58706-329-9) pp

105. Jurkowska RZ, Anspach N, Urbanke C, Jia D, Reinhardt R, Nellen W, Cheng X, Jeltsch A (2008) Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L. Nucleic Acids Res. 36, 6656-63 [Epub Oct 22]

104. Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008) The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455, 826-829 [Epub Sept 3] • see Editor's Summary • see News and Views by Jeltsch • Reading and writing DNA methylation • Emory University News Release: DNA Editing Tool Flips Its Target • How Cells Copy Epigenetic Markers: NIGMS-funded researchers have caught in action one of the tools mammalian cells use to maintain the pattern of methylation in DNA • Advanced Photon Source Science Highlights.

103. Subramanian K, Jia D, Kapoor-Vazirani P, Powell DR, Collins RE, Sharma D, Peng J, Cheng X, Vertino PM (2008) Regulation of estrogen receptor α by the SET7 lysine methyltransferase. Mol Cell 30, 336-347 • see Emory University News Release: Previously unseen switch regulates breast cancer response to estrogen

102. Rathert P, Dhayalan A, Murakami M, Zhang X, Tamas R, Jurkowska R, Komatsu Y, Shinkai Y, Cheng X, Jeltsch A (2008) Protein lysine methyltransferase G9a acts on non-histone targets. Nat Chem Biol. 4, 344-6 [Epub April 27] • see News and Views by Trojer and Reinberg • A gateway to study protein lysine methylation and F1000 evaluation • Emory University News Release: Epigenetic research uncovers new targets for modification enzymes • April 28, 2008 • NIGMS-funded researchers have discovered new molecular targets for an enzyme that modifies chromatin • Genetic Engineering & Biotechnical News: Investigators uncover nonhistone targets of methyltransferase

101.Cheng X, Blumenthal RM (2008) Mammalian DNA methyltransferases: a structural perspective. Structure 16, 341-50

100. Collins RE, Northrop JP, Horton JR, Lee DY, Zhang X, Stallcup MR, Cheng X (2008) The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat Struct Mol Biol. 15, 245-50 [Epub Feb 10] • see News and Views by Brent and Marmorstein • Ankyrin for methylated lysines and F1000 evaluation

99. Rathert P, Zhang X, Freund C, Cheng X, Jeltsch A (2008) Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays. Chem Biol 15, 5-11

98. Dhayalan A, Jurkowski TP, Laser H, Reinhardt R, Jia D, Cheng X, Jeltsch A (2008) Mapping of protein-protein interaction sites by the ‘Absence of Interference’ approach. J. Mol. Biol. 376, 1091-99 [Epub Dec 23 2007] • see F1000 evaluation

2007

97. Rathert P, Cheng X, Jeltsch A (2007) Continuous enzymatic assay for histone lysine methyltransferases. BioTechniques 43, 602-608

96. Osborne TC, Obianyo O, Zhang X, Cheng X, Thompson PR (2007) Protein arginine methyltransferase 1: positively charged residues in substrate peptides distal to the site of methylation are important for substrate binding and catalysis. Biochemistry 46, 13370-81 [Epub Oct 26]

95. Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X (2007) Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248-251 [Epub Aug 22] • News and Views by Ferguson-Smith and Greally • Epigenetics: Perceptive enzymes • Adding methyl groups to DNA is a way of regulating some genes and genomic sequences. Structural analysis reveals that the enzyme complex that mediates this process shows unexpected sequence specificity. • News Release: A Clue to Epigenetic Regulation • August 22, 2007 • Emory University • NIGMS-funded biochemists have discovered cues in DNA sequence that appear to signal a chemical modification that can differ depending on whether a gene is inherited from one's mother or father. • F1000 evaluation

94. Ooi SK, Qiu C, Bernstein E, Li K, Jia D, Yang Z, Erdjument-Bromage H, Tempst P, Lin SP, Allis CD, Cheng X, Bestor TH (2007) DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714-717. • F1000 evaluation.

93. Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi X, Gozani O, Cheng X, Shi Y (2007) Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448, 718-722. (view image) • News from Harvard Medical School: Zero Discovered in Code Controlling Gene Expression • August 31, 2007

92. Higashimoto K, Kuhn P, Desai D, Cheng X, Xu W (2007) Phosphorylation-mediated inactivation of coactivator-associated arginine methyltransferase 1. PNAS 104, 12318-12323 [Epub July 17]

91. Liebert K, Horton JR, Chahar S, Orwick M, Cheng X, Jeltsch A (2007) Two alternative conformations of AdoHcy bound to Escherichia coli DNA adenine methyltransferase and the implication of conformational changes in regulating the catalytic cycle. J. Biol. Chem. 282, 22848-22855 [Epub May 31] (view image)

90. Lee DY, Ianculescu I, Purcell D, Zhang X, Cheng X, Stallcup MR (2007) Surface-scanning mutational analysis of protein arginine methyltransferase 1: roles of specific amino acids in methyltransferase substrate specificity, oligomerization, and coactivator function. Mol Endocrinol. 21, 1381-1393 [Epub Apr 10]

89. Horton JR, Elgar SJ, Khan SI, Zhang X, Wade PA, Cheng X (2007) Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI. Proteins 67, 1198-1202 [Epub Mar 21]

88. Wu H, Horton JR, Battaile K, Allali-Hassani A, Martin F, Zeng H, Loppnau P, Vedadi M, Bochkarev A, Plotnikov AN, Cheng X (2007) Structural basis of allele variation of human thiopurine-S-methyltransferase. Proteins 67, 198-208 [Epub Jan 22]

87. Cheng X, Zhang X (2007) Structural dynamics of protein lysine methylation and demethylation. Mutat Res. 618, 102-115 [Epub Jan 21]

2006

86. Collins RE, Cheng X (2006) Structural and biochemical advances in mammalian RNAi. J. Cell. Biochem. 99, 1251-1266 [Epub 2006 Aug 22] (view cover image)

85. Mercante J, Suzuki K, Cheng X, Babitzke P, Romeo T (2006) Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance. J. Biol. Chem. 281, 31832-42. [Epub 2006 Aug 21]

84. Zhang X, Cheng X (2006) Structure of protein arginine methyltransferases. The Enzymes 24, 101-117 (ISBN 0121227251)

83. Schubert HL, Blumenthal RM, Cheng X (2006) Protein methyltransferases: their distribution among the five structural classes of AdoMet-dependent methyltransferases. The Enzymes 24, 1-26 (ISBN 0121227251)

82. Reyes-Turcu FE, Horton JR, Mullally JE, Heroux A, Cheng X, Wilkinson KD (2006) The Ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell 124, 1197-1208 • F1000 evaluation • Emory University News Release: Scientists Discover Unique Binding Method for Essential Cell Protein Ubiquitin

81. Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X (2006) Structure and substrate recognition of the E. coli DNA adenine methyltransferase. J. Mol. Biol. 358, 559-570

80. Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) DNA nicking by HinP1I endonuclease: bending, base flipping, and minor groove expansion. Nucleic Acids Res. 34, 939-948 (view image) • F1000 evaluation

2005

79. Horton JR, Sawada K, Nishibori M, Cheng X (2005) Structural basis for inhibition of histamine N-methyltransferase by diverse drugs. J. Mol. Biol. 353, 334-344. (view cover image)

78. Collins RE, Cheng X (2005) Structural domains in RNAi. FEBS Letters 579, 5841-5849 [Aug 15; Epub ahead of print]

77. Dillon SC, Zhang X, Trievel RC, Cheng X (2005) The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biology 6(8):227 [Epub 02 August 2005]

76. Gowher H, Zhang X, Cheng X, Jeltsch A (2005) Avidin plate assay system for enzymatic characterization of a histone lysine methyltransferase. Analytic Biochemistry 342, 287-291 [Epub May 31].

75. Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X (2005) Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of Dam methyltransferase. Cell 121, 349-361.

74. Yang Z, Horton JR, Maunus R, Wilson GG, Roberts RJ, Cheng X (2005) Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI. Nucleic Acids Res. 33, 1892-1901.

73. Cheng X, Collins RE, Zhang X (2005) Structural and sequence motifs of protein (histone) methylation enzymes. Annu Rev Biophys Biomol Struct. 34, 267-294 [Epub ahead of print]

72. Cheng X, Roberts RJ (2005) MHhaI and base flipping. In Virtual Text (www.ergito.com).

71. Collins RE, Tachibana M, Tamaru H, Smith KM, Jia D, Zhang X, Selker EU, Shinkai Y, Cheng X (2005) In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J. Biol. Chem. 280, 5563-5570 [Epub Dec. 6, 2004]

70. Amor JC, Swails J, Roy CR, Nagai H, Ingmundson A, Cheng X, Kahn RA (2005) The structure of RalF, an Arf guanine nucleotide exchangefactor from Legionella pneumophila, reveals the presence of a cap over the active site. J Biol Chem. 280, 1392-1400 [Epub Nov. 1, 2004] • F1000 evaluation

2004

69. Sawada K, Yang Z, Horton JR, Collins RE, Zhang X, Cheng X (2004) Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine79 methyltransferase. J. Biol. Chem. 279, 43296-43306 (Epub July 29, 2004). (view cover image)

68. Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Jr., Cheng, X (2004) Caught in the act: visualization of an intermediate in the DNA base flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res. 32, 3877-3886. (view cover image)

67. Yang Z, Shipman L, Zhang M, Anton BP, Roberts RJ, Cheng X (2004) Structural characterization and comparative phylogenetic analysis of E. coli HemK, a protein (N5)-glutamine methyltransferase. J. Mol. Biol. 340, 695-706.

66. Dong A, Zhou L, Zhang X, Stickel S, Roberts RJ, Cheng X (2004) Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions. Biol. Chem. 385, 373-379.(View PDB structure: 1SVU) (PDF)

65. Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh PB, Cheng X, Schubert I, Jenuwein T, Jacobsen SE (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112, 308-315.

64. Horton JR, Blumenthal RM, Cheng X (2004) Restriction endonucleases: structure of the conserved catalytic core and the role of metal ions in DNA cleavage. In Restriction Endonucleases. Serius: Nucleic Acids and Molecular Biology, Pingoud, Alfred (ed.) Springer-Verlag Berlin Heidelberg. Vol. 14. pp 361-392. (2004, XXVI, 443 p. 101 illus., 25 in color., Hardcover ISBN: 3-540-20502-0)

2003

63. Yang Z, Horton JR, Zhou L, Zhang XJ, Dong A, Zhang X, Schlagman SL, Kossykh V, Hattman S, Cheng X (2003) Structure of the bacteriophage T4 DNA adenine methyltransferase. Nature Struct. Biol. 10, 849-855. (View PDB structure: 1Q0S and 1Q0T) (view image)

62. Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X (2003) Structural basis for the product specificity of histone lysine methyltransferases. Mol. Cell 12, 177-185. (view PDB structure: 1PEG) (view image) (see preview by R. N. Dutnall (2003) Cracking the histone code: one, two, three methyls, you're out! Mol. Cell 12, 3-4) • F1000 evaluation

61. Schubert HL, Blumenthal RM, Cheng X (2003) Many paths to methyltransfer: a chronicle of convergence. Trends in Biochemical Sciences 28, 329-335.

60. Zhang X, Cheng X (2003) Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides. Structure 11, 509-520. (View PDB structure: 1ORI, 1OR8, 1ORH) (view image)

59. Tamaru H, Zhang X, McMillen D, Singh P, Nakayama J, Grewal S, Allis D, Cheng X, Selker EU (2003) Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nature Genetics 34, 75-79. • F1000 evaluation

58. P. Wu, C. Qiu, A. Sohail, X. Zhang, A. S. Bhagwat, X. Cheng (2003) Mismatch repair in methylated DNA: structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4. J. Biol. Chem. 278, 5285-91. (View PDB Structure: 1NGN) (view image)

2002

57. Blumenthal RM, Cheng X (2002) Restriction-modification systems. In: Modern Microbial Genetics, 2nd edition (Yasbin R.E. and Streips U.N., eds.). New York: Wiley. ISBN 0-471-38665-0 657pp

56. S. E. Whitehead, K. W. Jones, X. Zhang, X. Cheng, R. M. Terns, M. P. Terns (2002) Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1. J. Biol. Chem. 277, 48087-48093. • F1000 evaluation

55. J. Min, X. Zhang, X. Cheng, S. I. S. Grewal, R. Xu (2002) Structure of the SET domain histone lysine methyltransferase Clr4. Nature Struct. Biol. 9, 828-832. (View PDB Structure: 1MVH, 1MVX)

54. X. Zhang, H. Tamaru, S. I. Khan, J. R. Horton, L. J. Keefe, E. U. Selker, X. Cheng (2002) Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell 111, 117-127. (View PDB Structure: 1ML9) (view image) • F1000 evaluation

53. L. Zhou, X. Cheng, B. A. Connolly, M. J. Dickman, P. J. Hurd, D. P. Hornby (2002) Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases. J. Mol. Biol. 321, 591-599. (View PDB Structure: 1M0E)

52. Y.-H. Lee, S. S. Koh, X. Zhang, X. Cheng, M. R. Stallcup (2002) Synergy among nuclear receptor coactivators: selective requirement for protein methyltranferase and acetyltransferase activities. Mol. Cell. Biol. 22, 3621-3632. • F1000 evaluation

51. X. Cheng, R. M. Blumenthal (2002) Cytosines do it, thymines do it, even pseudouridines do it - base flipping by an enzyme that acts on RNA. Structure 10, 127-130.

50. D. M. Green, K. A. Marfatia, E. B. Crafton, X. Zhang, X. Cheng, A. H. Corbett (2002) Nab2p is required for poly(A) RNA export in Saccharomyces cerevisiae and is regulated by arginine methylation via Hmt1p. J. Biol. Chem. 277, 7752-7760.

49. C. Qiu, K. Sawada, X. Zhang, X. Cheng (2002) The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature Struct. Biol. 9, 217-224. (View PDB Structure: 1KHC)

2001

48. J. R. Horton, K. Sawada, M. Nishibori, X. Zhang, X. Cheng (2001) Two polymorphic forms of human histamine methyltransferase: structural, thermal and kinetic comparisons. Structure 9, 837-849. (View PDB Structure: 1JQD for Thr105 Polymorphic Variant, 1JQE for Ile105 Polymorphic Variant) (view cover image)

47. J. C. Amor, J. R. Horton, X. Zhu, Y. Wong, C. Sullards, D. Ringe, X. Cheng, R.A. Kahn (2001) Structures of yeast ARF2 and ARL1: distinct roles for the N-terminus in the structure and function of ARF family GTPases. J. Biol. Chem. 276, 42477-42484.

46. X. Cheng, R. J. Roberts (2001) AdoMet-dependent methylation, DNA methyltransferases, and base flipping. Nucleic Acids Res. 29, 3784-3795.

45. R. M. Blumenthal, X. Cheng (2001) A Taq attack displaces bases. Nature Struct. Biol. 8, 101-103.

44. A. Dong, J. A. Yoder, L. Zhou, X. Zhang, T. Bestor, X. Cheng (2001) Structure of human DNMT2, an enigmatic DNA methyltransferase homologue that displays denaturant-resistant binding to DNA. Nucleic Acids Res. 29, 439-448. (View PDB Structure: 1G55)

43. X. Cheng, R. J. Roberts (2001) Base flipping. Encyclopedia of Life Sciences / 2001 Nature Publishing Group / www.els.net

2000

42. G. Vilkaitis, A. Dong, E. Weinhold, X. Cheng, S. Klimasauskas (2000) Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J. Biol. Chem. 275, 38722-38730. (View PDB Structure: 1FJX, view moving structure)

41. J. R. Horton, X. Cheng (2000) PvuII Endonuclease contains two calcium ions in active sites. J. Mol. Biol. 300, 1051-1058. (View PDB Structure: 1EYU for complex at pH 4.6, 1F0O for pH 7.5 with calcium ions)

40. X. Zhang, L. Zhou, X. Cheng (2000) Crystal structure of the conserved core of the protein arginine methyltransferase PRMT3. EMBO J. 19, 3509-3519. (View PDB Structure: 1F3L)

1999

39. V. E. Marquez, A. Goddard, E. Alvarez, H. Ford Jr., J. K. Christman, G. Sheikhnejad, A. Brank, C. J. Marasco, J. R. Suffrin, M. O'Gara, X. Cheng (1999) Oligonucleotides containing 5, 6-dihydro-5-azacytosine at CpG sites can produce potent inhibition of DNA cytosine-C5-methyltransferase without covalently binding to the enzyme. Antisense & Nucleic Acid Drug Development, 9, 415-421.

38. E. B. Fauman, R. M. Blumenthal, and X. Cheng (1999) Structure and evolution of AdoMet-dependent methyltransferases. In X. Cheng, R. M. Blumenthal (eds.) AdoMet-dependent methyltransferases: structures and functions. (World Scientific, 1999 - 400 pages) pp. 1-38.

37. Y. Liu, W. Gong, C. C. Huang, W. Herr, X. Cheng (1999) Crystal structure of the conserved core of the HSV transcriptional regulatory protein VP16. Genes & Dev. 13, 1692-1703. (View PDB Structure: 16VP)

36. M. O'Gara, X. Zhang, R. J. Roberts, X. Cheng (1999) Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short nonspecific DNA oligonucleotide. J. Mol. Biol. 287, 201-210. (View PDB Structure: 2HMY, view moving structure)

35. G. Sheikhnejad, A. Brank, J. K. Christman, A. Goddard, E. Alvarez, H. Ford, Jr., V. E. Marquez, C. J. Marasco, J. R. Sufrin, M. O'Gara, X. Cheng (1999) Mechanism of inhibition of DNA-(cytosine C5) methyltransferases by oligodeoxyribonucleotides containing 5, 6-dihydro-5-azacytosine. J. Mol. Biol. 285, 2021-2034. (View PDB Structure: 10MH)

1998

34. J. R. Horton, H. G. Nastri, P. D. Riggs, X. Cheng (1998) Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis. J. Mol. Biol. 284, 1491-1504. (View PDB Structure: 3PVI)

33. J. R. Horton, J. Bonventre, X. Cheng (1998) How is modification of the DNA substrate recognized by the PvuII restriction endonuclease? Biol. Chem. 379, 451-458. (View PDB Structure: 2PVI) (Cover Image)

32. M. O'Gara, J. R. Horton, R. J. Roberts, X. Cheng (1998) Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Nature Struct. Biol. 5, 872-877. (View PDB Structure: 7MHT for G:A mismatch, 8MHT for G:U mismatch, 9MHT for G:abasic mismatch)

31. R. J. Roberts, X. Cheng (1998) Base flipping. Annu. Rev. Biochem. 67, 181-198.

1997

30. R. S. Lloyd, X. Cheng (1997) Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping. Biopolymers. 44, 139-151.

29. S. Kumar, J. R. Horton, G. D. Jones, R. T. Walker, R. J. Roberts, X. Cheng (1997) DNA containing 4'-thio-2-deoxycytidine inhibits the methylation of HhaI methyltransferase. Nucleic Acids Res. 25, 2773-2783. (View PDB Structure: 6MHT)

28. W. Gong, M. O'Gara, R. M. Blumenthal, X. Cheng (1997) Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25, 2702-2715. (View PDB Structure: 1BOO) (Cover Image)

27. M. O'Gara, G. M. Adams, W. Gong, R. Kobayashi, R. M. Blumenthal, X. Cheng (1997) Expression, purification, masspectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific). Eur J. Biochem. 247, 1009-1018.

26. R. Xu, L. Jokhan, X. Cheng, A. Mayeda, A. R. Krainer (1997) Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs. Structure 5, 559-570. (View PDB Structure: 1UP1)

25. R. Xu, C. Koch, Y. Liu, J. R. Horton, D. Knapp, K. Nasmyth, X. Cheng (1997) Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell cycle control of DNA synthesis. Structure 5, 349-358. (View PDB Structure: 1BM8)

1996

24. M. O'Gara, R. J. Roberts, X. Cheng (1996) A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase. J. Mol. Biol. 263, 597-606. (View PDB Structure: 5MHT, view moving structure) (Cover Image)

23. M. O'Gara, S. Klimasauskas, R. J. Roberts, X. Cheng (1996) Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes. J. Mol. Biol. 261, 634-645. (View PDB Structure: 3MHT for unmethylated DNA and 4MHT for fully-methylated DNA) (Cover Image)

22. X. Cheng, R. M. Blumenthal (1996) Finding a basis for flipping bases. Structure 4, 639-645.

21. R. Xu, G. Carmel, J. Kuret, X. Cheng (1996) Structural basis for selectivity of the isoquinoline sulfonamide family of protein kinase inhibitors. Proc. Natl. Acad. Sci. USA 93, 6308-6313. (View PDB Structure: 2CSN)

1995

20. R. Xu, G. Carmel, R.M. Sweet, J. Kuret, X. Cheng (1995) Crystal structure of casein kinase-1, a phosphate-directed protein kinase. EMBO J. 14, 1015-1023. (View PDB Structure: 1CSN) (Cover Image)

19. T. Malone, R.M. Blumenthal, X. Cheng (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol. 253, 618-632.

18. M. O'Gara, K. McCloy, T. Malone, X. Cheng (1995) Structure-based sequence alignment of three AdoMet-dependent methyltransferases. Gene 157, 135-138.

17. G. Schluckebier, M. O'Gara, W. Saenger, X. Cheng (1995) Universal catalytic domain structure of AdoMet-dependent methyltransferases. J. Mol. Biol. 247, 16-20.

16. X. Cheng (1995) Structure and function of DNA methyltransferases. Annu. Rev. Biophys. Biomol. Struct. 24, 293-318.

15. X. Cheng (1995) DNA modification by methyltransferases. Curr. Opin. Struc. Biol. 5, 4-10.

14. X. Cheng, K. Balendiran, I. Schildkraut, J. Anderson (1995) Crystal structure of the PvuII restriction endonuclease. Gene 157, 139-140.

1994

13. X. Cheng, K. Balendiran, I. Schildkraut, J. E. Anderson (1994) Structure of PvuII endonuclease with cognate DNA. EMBO J. 13, 3927-3935. (View PDB Structure: 1PVI, view moving structure)

12. X. Cheng, X. Zhang, J. W. Pflugrath, F. W. Studier (1994) The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase. Proc. Natl. Acad. Sci. USA 91, 4034-4038. (View PDB Structure: 1LBA)

11. G. Carmel, B. Leichus, X. Cheng, S. D. Patterson, U. Mirza, B. T. Chait, J. Kuret (1994) Expression, purification, crystallization, and preliminary X-ray analysis of casein kinase-1 from Schizosaccharomyces pombe. J. Biol. Chem. 269, 7304-7309.

10. S. Kumar, X. Cheng, S. Klimasauskas, S. Mi, J. Posfai, R. J. Roberts, G. G. Wilson (1994) The DNA (cytosine-5) Methyltransferases. Nucleic Acids Res. 22, 1-10. (Cover Image)

9. S. Klimasauskas, S. Kumar, R. J. Roberts, X. Cheng (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369. (View PDB Structure: 1MHT) (Cover Image)

1993

8. X. Cheng, S. Kumar, S. Klimasauskas, R. J. Roberts (1993) Crystal structure of the HhaI DNA methyltransferase. Cold Spring Harbor Symp. Quan. Biol. 58, 331-338.

7. X. Cheng, S. Kumar, J. Posfai, J. W. Pflugrath, R. J. Roberts (1993) Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell 74, 299-307. (View PDB Structure: 1HMY)

1992

6. S. Kumar, X. Cheng, J. W. Pflugrath, R. J. Roberts (1992). Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex. Biochemistry 31, 8648-8653.

1991

5. B. P. Schoenbom, X. Cheng (1991) The localization of solvent in protein crystals. In Protein: Structure, Dynamics and Design (ed. Renugopalakrishnan et al., ESCOM, Leiden) pp. 367-371.

4. X. Cheng, B. P. Schoenbom (1991) Repulsive restraints for hydrogen bonding in least-squares refinement of protein crystals. Acta Cryst. A47, 314-317.

3. X. Cheng, B. P. Schoenbom (1991) Neutron diffraction study of carbonmonoxymyoglobin. J. Mol. Biol. 220, 381-399.

1990

2. X. Cheng, B. P. Schoenbom (1990) Hydration in protein crystals. A neutron diffraction analysis of carbonmonoxymyoglobin. Acta Cryst. B46, 195-208. (View PDB Structure: 2MB5)

1981

1. Z. Xu, X. Cheng, et al. (1981) The mass of neutrino and the Schwarzchild's internal solution when l not equal to 0". Journal of Central China Normal University (Natural Sciences Edition, in Chinese), 2, 12-