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Brief Report

Large-scale global identification of protein lysine methylation in vivo

, &
Pages 477-485 | Received 03 Jan 2013, Accepted 03 Apr 2013, Published online: 17 Apr 2013

References

  • Kouzarides T. Histone methylation in transcriptional control. Curr Opin Genet Dev 2002; 12:198 - 209; http://dx.doi.org/10.1016/S0959-437X(02)00287-3; PMID: 11893494
  • Lachner M, Jenuwein T. The many faces of histone lysine methylation. Curr Opin Cell Biol 2002; 14:286 - 98; http://dx.doi.org/10.1016/S0955-0674(02)00335-6; PMID: 12067650
  • Sims RJ 3rd, Nishioka K, Reinberg D. Histone lysine methylation: a signature for chromatin function. Trends Genet 2003; 19:629 - 39; http://dx.doi.org/10.1016/j.tig.2003.09.007; PMID: 14585615
  • Greer EL, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 2012; 13:343 - 57; http://dx.doi.org/10.1038/nrg3173; PMID: 22473383
  • Simon JA, Lange CA. Roles of the EZH2 histone methyltransferase in cancer epigenetics. Mutat Res 2008; 647:21 - 9; http://dx.doi.org/10.1016/j.mrfmmm.2008.07.010; PMID: 18723033
  • Richon VM, Johnston D, Sneeringer CJ, Jin L, Majer CR, Elliston K, et al. Chemogenetic analysis of human protein methyltransferases. Chem Biol Drug Des 2011; 78:199 - 210; http://dx.doi.org/10.1111/j.1747-0285.2011.01135.x; PMID: 21564555
  • Chuikov S, Kurash JK, Wilson JR, Xiao B, Justin N, Ivanov GS, et al. Regulation of p53 activity through lysine methylation. Nature 2004; 432:353 - 60; http://dx.doi.org/10.1038/nature03117; PMID: 15525938
  • Huang J, Perez-Burgos L, Placek BJ, Sengupta R, Richter M, Dorsey JA, et al. Repression of p53 activity by Smyd2-mediated methylation. Nature 2006; 444:629 - 32; http://dx.doi.org/10.1038/nature05287; PMID: 17108971
  • Luttun A, Tjwa M, Carmeliet P. Placental growth factor (PlGF) and its receptor Flt-1 (VEGFR-1): novel therapeutic targets for angiogenic disorders. Ann N Y Acad Sci 2002; 979:80 - 93; http://dx.doi.org/10.1111/j.1749-6632.2002.tb04870.x; PMID: 12543719
  • Kouskouti A, Scheer E, Staub A, Tora L, Talianidis I. Gene-specific modulation of TAF10 function by SET9-mediated methylation. Mol Cell 2004; 14:175 - 82; http://dx.doi.org/10.1016/S1097-2765(04)00182-0; PMID: 15099517
  • Kurash JK, Lei H, Shen Q, Marston WL, Granda BW, Fan H, et al. Methylation of p53 by Set7/9 mediates p53 acetylation and activity in vivo. Mol Cell 2008; 29:392 - 400; http://dx.doi.org/10.1016/j.molcel.2007.12.025; PMID: 18280244
  • Rathert P, Dhayalan A, Murakami M, Zhang X, Tamas R, Jurkowska R, et al. Protein lysine methyltransferase G9a acts on non-histone targets. Nat Chem Biol 2008; 4:344 - 6; http://dx.doi.org/10.1038/nchembio.88; PMID: 18438403
  • Levy D, Liu CL, Yang Z, Newman AM, Alizadeh AA, Utz PJ, et al. A proteomic approach for the identification of novel lysine methyltransferase substrates. Epigenetics Chromatin 2011; 4:19; http://dx.doi.org/10.1186/1756-8935-4-19; PMID: 22024134
  • Ballif BA, Carey GR, Sunyaev SR, Gygi SP. Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. J Proteome Res 2008; 7:311 - 8; http://dx.doi.org/10.1021/pr0701254; PMID: 18034455
  • Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 2009; 325:834 - 40; http://dx.doi.org/10.1126/science.1175371; PMID: 19608861
  • Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, et al. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell 2011; 44:325 - 40; http://dx.doi.org/10.1016/j.molcel.2011.08.025; PMID: 21906983
  • Kim SC, Sprung R, Chen Y, Xu Y, Ball H, Pei J, et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 2006; 23:607 - 18; http://dx.doi.org/10.1016/j.molcel.2006.06.026; PMID: 16916647
  • Pesavento JJ, Bullock CR, LeDuc RD, Mizzen CA, Kelleher NL. Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry. J Biol Chem 2008; 283:14927 - 37; http://dx.doi.org/10.1074/jbc.M709796200; PMID: 18381279
  • Chin HG, Estève PO, Pradhan M, Benner J, Patnaik D, Carey MF, et al. Automethylation of G9a and its implication in wider substrate specificity and HP1 binding. Nucleic Acids Res 2007; 35:7313 - 23; http://dx.doi.org/10.1093/nar/gkm726; PMID: 17962312
  • Patnaik D, Chin HG, Estève PO, Benner J, Jacobsen SE, Pradhan S. Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase. J Biol Chem 2004; 279:53248 - 58; http://dx.doi.org/10.1074/jbc.M409604200; PMID: 15485804
  • Collins RE, Tachibana M, Tamaru H, Smith KM, Jia D, Zhang X, et al. In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J Biol Chem 2005; 280:5563 - 70; http://dx.doi.org/10.1074/jbc.M410483200; PMID: 15590646
  • Ong SE, Mann M. Identifying and quantifying sites of protein methylation by heavy methyl SILAC. Curr Protoc Protein Sci 2006; Chapter 14:Unit 14 9.
  • Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A. UniProtKB/Swiss-Prot. Methods Mol Biol 2007; 406:89 - 112; PMID: 18287689
  • Beck HC, Nielsen EC, Matthiesen R, Jensen LH, Sehested M, Finn P, et al. Quantitative proteomic analysis of post-translational modifications of human histones. Mol Cell Proteomics 2006; 5:1314 - 25; http://dx.doi.org/10.1074/mcp.M600007-MCP200; PMID: 16627869
  • Donlin LT, Andresen C, Just S, Rudensky E, Pappas CT, Kruger M, et al. Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization. Genes Dev 2012; 26:114 - 9; http://dx.doi.org/10.1101/gad.177758.111; PMID: 22241783
  • UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012; 40:Database issue D71 - 5; http://dx.doi.org/10.1093/nar/gkr981; PMID: 22102590
  • Kahns S, Lund A, Kristensen P, Knudsen CR, Clark BF, Cavallius J, et al. The elongation factor 1 A-2 isoform from rabbit: cloning of the cDNA and characterization of the protein. Nucleic Acids Res 1998; 26:1884 - 90; http://dx.doi.org/10.1093/nar/26.8.1884; PMID: 9518480
  • Pang CN, Gasteiger E, Wilkins MR. Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. BMC Genomics 2010; 11:92; http://dx.doi.org/10.1186/1471-2164-11-92; PMID: 20137074
  • Boisvert FM, Côté J, Boulanger MC, Richard S. A proteomic analysis of arginine-methylated protein complexes. Mol Cell Proteomics 2003; 2:1319 - 30; http://dx.doi.org/10.1074/mcp.M300088-MCP200; PMID: 14534352
  • Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, et al. Systematic functional prioritization of protein posttranslational modifications. Cell 2012; 150:413 - 25; http://dx.doi.org/10.1016/j.cell.2012.05.036; PMID: 22817900
  • Canman CE, Lim DS. The role of ATM in DNA damage responses and cancer. Oncogene 1998; 17:3301 - 8; http://dx.doi.org/10.1038/sj.onc.1202577; PMID: 9916992
  • Fernandez-Capetillo O, Chen HT, Celeste A, Ward I, Romanienko PJ, Morales JC, et al. DNA damage-induced G2-M checkpoint activation by histone H2AX and 53BP1. Nat Cell Biol 2002; 4:993 - 7; http://dx.doi.org/10.1038/ncb884; PMID: 12447390
  • Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007; 316:1160 - 6; http://dx.doi.org/10.1126/science.1140321; PMID: 17525332
  • Sun Y, Xu Y, Roy K, Price BD. DNA damage-induced acetylation of lysine 3016 of ATM activates ATM kinase activity. Mol Cell Biol 2007; 27:8502 - 9; http://dx.doi.org/10.1128/MCB.01382-07; PMID: 17923702
  • Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006; 127:635 - 48; http://dx.doi.org/10.1016/j.cell.2006.09.026; PMID: 17081983
  • Dephoure N, Zhou C, Villén J, Beausoleil SA, Bakalarski CE, Elledge SJ, et al. A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A 2008; 105:10762 - 7; http://dx.doi.org/10.1073/pnas.0805139105; PMID: 18669648
  • Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, et al. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci Signal 2009; 2:ra46; http://dx.doi.org/10.1126/scisignal.2000007; PMID: 19690332
  • Takawa M, Cho HS, Hayami S, Toyokawa G, Kogure M, Yamane Y, et al. Histone lysine methyltransferase SETD8 promotes carcinogenesis by deregulating PCNA expression. Cancer Res 2012; 72:3217 - 27; http://dx.doi.org/10.1158/0008-5472.CAN-11-3701; PMID: 22556262
  • Komatsu S, Imoto I, Tsuda H, Kozaki KI, Muramatsu T, Shimada Y, et al. Overexpression of SMYD2 relates to tumor cell proliferation and malignant outcome of esophageal squamous cell carcinoma. Carcinogenesis 2009; 30:1139 - 46; http://dx.doi.org/10.1093/carcin/bgp116; PMID: 19423649
  • Zee BM, Levin RS, Xu B, LeRoy G, Wingreen NS, Garcia BA. In vivo residue-specific histone methylation dynamics. J Biol Chem 2010; 285:3341 - 50; http://dx.doi.org/10.1074/jbc.M109.063784; PMID: 19940157
  • Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, et al. Directed proteomic analysis of the human nucleolus. Curr Biol 2002; 12:1 - 11; http://dx.doi.org/10.1016/S0960-9822(01)00650-9; PMID: 11790298
  • Shi X, Kachirskaia I, Yamaguchi H, West LE, Wen H, Wang EW, et al. Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol Cell 2007; 27:636 - 46; http://dx.doi.org/10.1016/j.molcel.2007.07.012; PMID: 17707234
  • Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, et al. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 2005; 23:94 - 101; http://dx.doi.org/10.1038/nbt1046; PMID: 15592455
  • Rappsilber J, Ishihama Y, Mann M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem 2003; 75:663 - 70; http://dx.doi.org/10.1021/ac026117i; PMID: 12585499
  • Li D, Fu Y, Sun R, Ling CX, Wei Y, Zhou H, et al. pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry. Bioinformatics 2005; 21:3049 - 50; http://dx.doi.org/10.1093/bioinformatics/bti439; PMID: 15817687
  • Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R. The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004; 4:1985 - 8; http://dx.doi.org/10.1002/pmic.200300721; PMID: 15221759
  • Elias JE, Haas W, Faherty BK, Gygi SP. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2005; 2:667 - 75; http://dx.doi.org/10.1038/nmeth785; PMID: 16118637
  • Horton P, Nakai K. Better prediction of protein cellular localization sites with the k nearest neighbors classifier. Proc Int Conf Intell Syst Mol Biol 1997; 5:147 - 52; PMID: 9322029
  • Adamczak R, Porollo A, Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 2005; 59:467 - 75; http://dx.doi.org/10.1002/prot.20441; PMID: 15768403
  • Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005; 21:3448 - 9; http://dx.doi.org/10.1093/bioinformatics/bti551; PMID: 15972284

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