Yingming Zhao, Ph.D.

References

2012

Liu, J., Yan, J., Jiang, S., Wen, J., Chen, L., Zhao, Y., Lin, A.,Site-specific ubiquitination is required for relieving the transcription factor Miz1-mediated suppression on TNF-α-induced JNK activation and inflammation. Proc Natl Acad Sci U S A,2012. 109(1): p. 191-196.

2011

Tan, M., Luo, H., Lee, S., Jin, F., Yang, J.-S., Montellier, E., Buchou,T., Cheng, Z., Rousseaux, S., Rajagopal, N., Lu, Z., Ye, Z., Zhu, Q., Wysocka, J., Ye, Y., Khochbin, S., Ren, B., Zhao, Y., Identification of 67 histone marks and histone lysine crotonylation as a new type of Histone modification. Cell, 2011. 146: p.1016-1028.

Zhang, Z., Tan, M., Xie, Z., Dai, L., Chen, Y., and Zhao, Y., Identification of lysine   succinylation as a new post-translational modification. Nature Chem Biol,2011. 7(1): p. 58-63.

Peng, C., Lu, Z., Xie, Z., Cheng, Z., Chen, Y., Tan, M., Luo, H., Zhang, Y., He, W., Yang, K., Zwaans, B.M. M., Tishkoff, D., Ho, L., Lombard, D., He, T.-C., Dai, J., Verdin, E., Ye, Y., Zhao, Y., The first identification of lysine malonylation substrates and its regulatory enzyme. Mol Cell Proteomics, 2011.10 (12):M111.012658.

Lu, J.-Y.,Lin, Y.-Y.,Sheu, J.-C., Wu, J.-T.,Lee, F.-J., Chen, Y.,Lin M.-I,Chiang, F.-T., Tai, T.-Y.,Berger, S. L.,Zhao, Y., Tsai K.-S.,Zhu, H.,Chuang, L.-M.,and Boeke, J. D., Acetylation of Yeast AMPK Controls Intrinsic Aging Independently of Caloric Restriction. Cell, 2011. 146: p. 969-979.

Lu, Z., Cheng, Z., Zhao, Y., Volchenboum ,S.L., Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation.PLoS One, 2011. 6(12): p. e28228.

Li, X., Wang, Q., Pan, N., Lee, S., Zhao, Y., Chait, B., Yue, Z. Phosphorylation-Dependent 14-3-3 Binding to LRRK2 Is Impaired by Common Mutations of Familial Parkinson’s Disease. PLoS One, 2011. 6(3): p. e17153

Ghosh, S., Zhang, J., Zhao, Y., DePamphilis,M.L., and Vassilev,A.P.,Assembly of the human origin recognition complex occurs through independent nuclear localization of its components.J Biol Chem, 2011.286(27): p.23831-23841.

Samant, S.A., Courson, D.S., Sundaresan, N.R., Pillai, V.B., Tan, M., Zhao, Y., Shroff, S.G., Rock, R.S. and Gupta, M.P., HDAC3-dependent reversible lysine acetylation of cardiac myosin heavy chain isoforms modulates their enzymatic and motor activity. J Biol Chem, 2011. 286(7): p.5567-77.

Song, H., Li, C.-W., Labaff, A.M., Lim, S.-O., Li, L., Kan, S.-F., Chen, Y., Zhang, K., Lang, J., Xie, X., Wang, Y., Huo, L., Hsu, S.-C., Chen, X., Zhao, Y., Hung, M.-C., Acetylation of EGF receptor contributes to tumor cell resistance to Histone deacetylase inhibitors. Biochemical and Biophysical Research Communications,2011. 404(1): p. 68–73.

2010

Bajpai, R., Chen, D.A., Rada-Iglesias, A., Zhang, J., Xiong, Y., Helms, J., Chang, C.P., Zhao,Y., Swigut, T., and Wysocka, J., CHD7 cooperates with PBAF to control multipotent neural crest formation. Nature,2010. 463: p.958-62.

Kuo, H.P., Lee, D.F., Chen, C.T., Liu, M., Chou, C.K., Lee, H.J., Du, Y., Xie, X., Wei, Y., Xia, W., Zhang, W., Yang, J.-Y., Yen, C.-J., Huang, T.-H., Tan, M., Xing, G., Zhao, Y., Lin,C.-H., Tsai, S.-F., Fidler, I. J., and Hung, M.-C., ARD1 stabilization of TSC2 suppresses tumorigenesis through the mTOR signaling pathway. Sci Signal, 2010.3(108): p.ra9.

Zhang, J., Chen, Y., Zhang, Z., Xing, G., Wysocka, J., and Zhao, Y., MS/MS/MS reveals false positive identification of histone serine methylation. J Proteome Res,2010. 9: p.585-94.

Lee, S., Chen, Y., Luo, H., Wu, A.A., Wilde, M., Schumacker, P., and Zhao, Y., The first global screening of protein substrates bearing protein-bound 3,4-dihydroxyphenylalanine in E. coli and human mitochondria. J Proteome Research,2010. 9: p. 5705-14.

Zhang, K., Chen, Y., Zhang, Z., Tao, S., Zhu, H., and Zhao, Y., Unrestrictive identification of non-phosphorylation PTMs in yeast kinases by MS and PTMap. Proteomics,2010. 10: p. 896-903.

Li, L., Sun, L., Gao, F., Jiang, J., Yang, Y., Li, C., Gu, J., Wei, Z., Yang, A., Lu, R., Ma, Y., Tang, F., Kwon, S.W., Zhao, Y., Li, J., and Jin, Y., Stk40 links the pluripotency factor Oct4 to the Erk/MAPK pathway and controls extraembryonic endoderm differentiation. Proc Natl Acad Sci U S A,2010. 107(4): p.1402-1407.

Zeng, S.X., Li, Y., Jin, Y., Zhang, Q., Keller, D.M., McQuaw, C.M., Barklis, E., Stone, S., Hoatlin, M., Zhao, Y., Lu, H., Structure-specific recognition protein 1 facilitates microtubule growth and bundling required for mitosis. Mol Cell Biol,2010. 30(4): p.935-947.

Heise, C.J., Xu, B.E., Deaton, S.L., Cha, S.K., Cheng, C.J., Earnest, S., Sengupta, S., Juang, Y.C., Stippec, S., Xu, Y., Zhao, Y., Huang, C.L., Cobb. M.H., Serum and glucocorticoid-induced kinase (SGK) 1 and the epithelial sodium channel are regulated by multiple with no lysine (WNK) family members. J Biol Chem,2010. 285(33): p.25161-25167.

He, B.-C., Gao, J.-L., Zhang, B.-Q., Luo, Q., Shi, Q., Kim, S.H., Huang, E., Gao, Y., Yang, K., Wagner, E.R., Wang, L., Tang, N., Luo, J., Liu, X., Li, M., Bi, Y., Shen, J., Luther, G., Hu, N., Zhou, Q., Luu, H.H., Haydon, R.C., Zhao, Y., and He, T.-C., Tetrandrine Inhibits Wnt/b-Catenin Signaling and Suppresses Tumor Growth of Human Colorectal Cancer. Molecular Pharmacology,2010. 79(2): p.211-219.

2009

Chen, Y., Chen, W., Cobb, M.H. and Zhao, Y., PTMap--a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc Natl Acad Sci U S A, 2009. 106(3): p. 761-6.

Cheng, Z., Tang, Y., Chen, Y., Kim, S., Liu, H., Li, S.S., Gu, W. and Zhao, Y., Molecular characterization of propionyllysines in non-histone proteins. Mol Cell Proteomics,2009. 8(1): p. 45-52.

Zhang, J., Sprung, R., Pei, J., Tan, X., Kim, S., Zhu, H., Liu, C.F., Grishin, N.V. and Zhao, Y., Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics,2009. 8(2): p. 215-25.

Lin, Y.Y., Lu, J.Y., Zhang, J., Walter, W., Dang, W., Wan, J., Tao, S.C., Qian, J.,Zhao, Y., Boeke, J.D., Berger, S.L. and Zhu, H., Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell, 2009. 136(6): p. 1073-84.

Peng, J.C., Valouev, A., Swigut, T., Zhang, J., Zhao, Y., Sidow, A. and Wysocka, J., Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell, 2009. 139(7): p. 1290-302.

Chan, D.W., Wang, Y., Wu, M., Wong, J., Qin, J. and Zhao, Y., Unbiased proteomic screen for binding proteins to modified lysines on histone H3. Proteomics, 2009. 9(9): p. 2343-54.

Zhang, K., Chen, Y., Zhang, Z. and Zhao, Y., Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software. J Proteome Res,2009. 8(2): p. 900-6.

Chen, Y., Zhang, J., Xing, G. and Zhao, Y., Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra. J Proteome Res, 2009. 8(6): p. 3141-7.

Zhao, Y. and Jensen, O.N., Modification-specific proteomics: Strategies for characterization of post-translational modifications using enrichment techniques. Proteomics, 2009. 9(20): p. 4632-41.

Basu, A., Rose, K.L., Zhang, J., Beavis, R.C., Ueberheide, B., Garcia, B.A., Chait, B., Zhao, Y., Hunt, D.F., Segal, E., Allis, C.D. and Hake, S.B., Proteome-wide prediction of acetylation substrates. Proc Natl Acad Sci U S A, 2009. 106(33): p. 13785-13790.

Rosse, C., Formstecher, E., Boeckeler, K., Zhao, Y., Kremerskothen, J., White, M.D., Camonis, J.H. and Parker, P.J., An aPKC-exocyst complex controls paxillin phosphorylation and migration through localised JNK1 activation. PLoS Biol, 2009. 7(11): p. e1000235.

Chon, H., Vassilev, A., DePamphilis, M.L., Zhao, Y., Zhang, J., Burgers, P.M., Crouch, R.J. and Cerritelli, S.M., Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex. Nucleic Acids Res, 2009. 37(1): p. 96-110.

Chen, W., Chen, Y., Xu, B.E., Juang, Y.C., Stippec, S., Zhao, Y. and Cobb, M.H., Regulation of a third conserved phosphorylation site in SGK1. J Biol Chem, 2009. 284(6): p. 3453-60.

2008

Tang, Y., Zhao, W., Chen, Y., Zhao, Y. and Gu, W., Acetylation is indispensable for p53 activation. Cell, 2008. 133(4): p. 612-26.

Xing, G., Zhang, J., Chen, Y. and Zhao, Y., Identification of four novel types of in vitro protein modifications. J Proteome Res, 2008. 7(10): p. 4603-8.

Sprung, R., Chen, Y., Zhang, K., Cheng, D., Zhang, T., Peng, J. and Zhao, Y., Identification and validation of eukaryotic aspartate and glutamate methylation in proteins. J Proteome Res, 2008. 7(3): p. 1001-6.

Lin, Y.Y., Qi, Y., Lu, J.Y., Pan, X., Yuan, D.S., Zhao, Y., Bader, J.S. and Boeke, J.D., A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes Dev, 2008. 22(15): p. 2062-74.

Jung, S.Y., Li, Y., Wang, Y., Chen, Y., Zhao, Y. and Qin, J., Complications in the assignment of 14 and 28 Da mass shift detected by mass spectrometry as in vivo methylation from endogenous proteins. Anal Chem, 2008. 80(5): p. 1721-9.

 Deng, H., Yu, F., Chen, J., Zhao, Y., Xiang, J. and Lin, A., Phosphorylation of Bad at Thr-201 by JNK1 promotes glycolysis through activation of phosphofructokinase-1. J Biol Chem, 2008. 283(30): p. 20754-60.

2007

Chen, Y., Sprung, R., Tang, Y., Ball, H., Sangras, B., Kim, S.C., Falck, J.R., Peng, J., Gu, W. and Zhao, Y., Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics, 2007. 6(5): p. 812-9.

Lee, J., Xu, Y., Chen, Y., Sprung, R., Kim, S.C., Xie, S. and Zhao, Y., Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS. Mol CellProteomics, 2007. 6(4): p. 669-76.

Xu, Y., Sprung, R., Kwon, S.W., Kim, S.C. and Zhao, Y., Isolation of phosphopeptides by pI-difference-based electrophoresis. J Proteome Res, 2007. 6(3): p. 1153-7.

Chang, B., Chen, Y., Zhao, Y. and Bruick, R.K., JMJD6 is a histone arginine demethylase. Science, 2007. 318(5849): p. 444-7.

Kang, J., Chen, Y., Zhao, Y. and Yu, H., Autophosphorylation-dependent activation of human Mps1 is required for the spindle checkpoint. Proc Natl Acad Sci U S A, 2007. 104(51): p. 20232-7.

Raman, M., Earnest, S., Zhang, K., Zhao, Y. and Cobb, M.H., TAO kinases mediate activation of p38 in response to DNA damage. Embo J, 2007. 26(8): p. 2005-14.

Bartz, R., Zehmer, J.K., Zhu, M., Chen, Y., Serrero, G., Zhao, Y. and Liu, P., Dynamic activity of lipid droplets: protein phosphorylation and GTP-mediated protein translocation. J Proteome Res, 2007. 6(8): p. 3256-65.

Ganesan, A.K., Kho, Y., Kim, S.C., Chen, Y., Zhao, Y. and White, M.A., Broad spectrum identification of SUMO substrates in melanoma cells. Proteomics, 2007. 7(13): p. 2216-2221.

Li, H., Zhang, Z., Wang, B., Zhang, J., Zhao, Y. and Jin, Y., The Wwp2-mediated Ubiquitination of the RNA Polymerase II Large Subunit in Mouse Embryonic Pluripotent Stem Cells. Mol Cell Biol, 2007. 27(15): p. 5296-5305.

2006

Kim, S.C., Sprung, R., Chen, Y., Xu, Y., Ball, H., Pei, J., Cheng, T., Kho, Y., Xiao, H., Xiao, L., Grishin, N.V., White, M., Yang, X.J. and Zhao, Y., Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell, 2006. 23(4): p. 607-18.

Nandi, A., Sprung, R., Barma, D.K., Zhao, Y., Kim, S.C., Falck, J.R. and Zhao, Y., Global identification of O-GlcNAc-modified proteins. Anal Chem, 2006. 78(2): p. 452-8.

Chien, Y., Kim, S., Bumeister, R., Loo, Y.M., Kwon, S.W., Johnson, C.L., Balakireva, M.G., Romeo, Y., Kopelovich, L., Gale, M., Jr., Yeaman, C., Camonis, J.H., Zhao, Y. and White, M.A., RalB GTPase-mediated activation of the IkappaB family kinase TBK1 couples innate immune signaling to tumor cell survival. Cell, 2006. 127(1): p. 157-70.

Qiu, Y., Zhao, Y., Becker, M., John, S., Parekh, B.S., Huang, S., Martinez, E.D., Chen, Y., Lu, H., Adkins, N.L., Georgel, P.T., Schiltz, P.L. and Hager, G.L., HDAC1 Acetylation is Linked to Progressive Modulation of Steroid Receptor Induced Gene Transcription. Mol Cell, 2006. 22(5): p. 669-679.

Kim, S.C., Chen, Y., Mirza, S., Xu, Y., Lee, J., Liu, P. and Zhao, Y., A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea. J Proteome Res, 2006. 5(12): p. 3446-52.

Anselmo, A.N., Earnest, S., Chen, W., Juang, Y.C., Kim, S.C., Zhao, Y. and Cobb, M.H., WNK1 and OSR1 regulate the Na+, K+, 2Cl- cotransporter in HeLa cells. Proc Natl Acad Sci U S A, 2006. 103(29): p. 10883-8.

McMahon, K.A., Zhu, M., Kwon, S.W., Liu, P., Zhao, Y. and Anderson, R.G., Detergent-free caveolae proteome suggests an interaction with ER and mitochondria. Proteomics, 2006. 6(1): p. 143-52.

Radichev, I., Kwon, S.W., Zhao, Y., DePamphilis, M.L. and Vassilev, A., Genetic analysis of human Orc2 reveals specific domains that are required in vivo for assembly and nuclear localization of the origin recognition complex. J Biol Chem, 2006. 281(32): p. 23264-73.

Binns, D., Januszewski, T., Chen, Y., Hill, J., Markin, V.S., Zhao, Y., Gilpin, C., Chapman, K.D., Anderson, R.G. and Goodman, J.M., An intimate collaboration between peroxisomes and lipid bodies. J Cell Biol, 2006. 173(5): p. 719-31.