Publications

2016

  • Zhou, T., Chung, Y., Chen, J., Chen, Y., Site-specific Identification of Lysine Acetylation Stoichiometries in Mammalian Cells. J Proteome Res 15, 1103-1113. (2016)
  • Chen, Y., Quantitative Analysis of the Sirt5-Regulated Lysine Succinylation Proteome in Mammalian Cells. Methods Molecular Biology, Vol. 1410, Salvatore Sechi (Eds.) (2016)
  • Fang, D., Gan, H., Lee, J.H., Han, J., Wang, Z., Riester, S.M., Jin, L., Chen, J., Zhou, H., Wang, J., Zhang, H., Yang, N., Bradley, E.W., Ho, T.H., Rubin, B.P., Bridge, J.A., Thibodeau, S.N., Ordog, T., Chen, Y., van Wijnen, A.J., Oliveira, A.M., Xu, R.M., Westendorf, J.J., Zhang, Z. The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas. Science 352(6291):1344-1348 (2016)
  • Liu, K., Li, F., Han, H., Chen, Y., Mao, Z., Luo, J., Zhao, Y., Zheng, B., Gu, W., Zhao, W. Parkin Regulates the Activity of Pyruvate Kinase M2. J. Biol. Chem. 291(19):10307-10317 (2016).

 

2015

  • Head, S.A., Shi, W., Zhao, L., Gorshkov, K., Pasunooti, K., Chen, Y., Deng, Z., Li, R.J., Shim, J.S., Tan, W., Hartung, T., Zhang, J., Zhao, Y., Colombini, M., Liu, J.O. Antifungal drug itraconazole targets VDAC1 to modulate the AMPK/mTOR signaling axis in endothelial cells. Proc Natl Acad Sci U S A 112, E7276–E7285 (2015).

 

2014

  • Tang, S., Huang, G., Fan, W., Chen, Y., Ward, J.M., Xu, X., Xu, Q., Kang, A., McBurney, M.W., Fargo, D.C., Hu, G., Baumgart-Vogt, E., Zhao, Y., Li, X. SIRT1-Mediated Deacetylation of CRABPII Regulates Cellular Retinoic Acid Signaling and Modulates Embryonic Stem Cell Differentiation. Cell 55, 843-855 (2014).
  • Tan, M., Peng, C., Anderson, K.A., Chhoy, P., Xie, Z., Dai, L., Park, J., Chen, Y., Huang, H., Zhang, Y., Ro, J., Wagner, G.R., Green, M.F., Madsen, A.S., Schmiesing, J., Peterson, B.S., Xu, G., Ilkayeva, O.R., Muehlbauer, M.J., Braulke, T., Mühlhausen, C., Backos, D.S., Olsen, C.A., McGuire, P.J., Pletcher, S.D., Lombard, D.B., Hirschey, M.D. & Zhao, Y. Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. Cell Metab 19, 605-617 (2014).
  • Dai, L., Peng, C., Montellier, E., Lu, Z., Chen, Y., Ishii, H., Debernardi, A., Buchou, T., Rousseaux, S., Jin, F., Sabari, B.R., Deng, Z., Allis, C.D., Ren, B., Khochbin, S. & Zhao, Y. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat Chem Biol 10, 365-370 (2014).

 

2013

  • Park, J.#, Chen, Y.#, Tishkoff, D.X., Peng, C., Tan, M., Dai, L., Xie, Z., Zhang, Y., Zwaans, B.M.M., Skinner, M.E., Lombard, D.B. & Zhao, Y. Sirt5-mediated Lys desuccinylation regulates diverse metabolic pathways. Mol Cell 50, 919-930 (2013) (# equal contribution).
  • Colak, G., Xie, Z., Zhu, A.Y., Dai, L., Lu, Z., Zhang, Y., Wan, X., Chen, Y., Cha, Y.H., Lin, H., Zhao, Y. & Tan, M. Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. Mol Cell Proteomics 12, 3509-3520 (2013).
  • Chen, Y., Colak, G. & Zhao, Y. SILAC-based quantification of Sirt1-response Lys acetylome. In M. Hirshey (Ed.) Methods Mol Biol., Sirtuin Ed. 1077, 105-120 (2013).
  • Dobbin, M.M., Madabhushi, R., Pan, L., Chen, Y., Kim, D., Gao, J., Ahanonu, B., Pao, P.C., Qiu, Y., Zhao, Y. & Tsai, L.H. SIRT1 collaborates with ATM and HDAC1 to maintain genomic stability in neurons. Nat Neurosci 8, 1008-1015 (2013).
  • Lee, S.*, Tan, M., Dai, L., Kwon, O.K., Yang, J., Zhao, Y. & Chen, Y.* MS/MS of synthetic peptide is not sufficient to confirm new types of protein modifications. J Proteome Res 12, 1007-1013 (2013) (* corresponding authors).
  • Liao, B., Zhong, X., Xu, H., Xiao, F., Fang, Z., Gu, J., Chen, Y., Zhao, Y. & Jin, Y. Itch, an e3 ligase of Oct4, is required for embryonic stem cell self-renewal and pluripotency induction. J Cell Physiol 228, 1443-1451 (2013).

 

2012

  • Chen, Y., Zhao, W., Yang, J.S., Cheng, Z., Luo, H., Lu, Z., Tan, M., Gu, W. & Zhao, Y. Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways. Mol Cell Proteomics 11, 1048-1062 (2012).

 

2011

  • Peng, C., Lu, Z., Xie, Z., Cheng, Z., Chen, Y., Tan, M., Luo, H., Zhang, Y., He, W., Yang, K., Zwaans, B.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 10, M111.012658 (2011).
  • 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. & Boeke, J.D. Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell 146, 969-979 (2011).
  • Zhang, Z., Tan, M., Xie, Z., Dai, L., Chen, Y. & Zhao, Y. Identification of lysine succinylation as a new post-translational modification. Nat Chem Biol 7, 58-63 (2011).
  • Song, H., Li, C.W., Labaff, A.M., Lim, S.O., Li, L.Y., Kan, S.F., Chen, Y., Zhang, K., Lang, J., Xie, X., Wang, Y., Huo, L.F., Hsu, S.C., Chen, X., Zhao, Y. & Hung, M.C. Acetylation of EGF receptor contributes to tumor cell resistance to histone deacetylase inhibitors. Biochem Biophys Res Commun 404, 68-73 (2011).

 

2010

  • Lee, S., Chen, Y., Luo, H., Wu, A.A., Wilde, M., Schumacker, P.T. & Zhao, Y. The first global screening of protein substrates bearing protein-bound 3,4-Dihydroxyphenylalanine in Escherichia coli and human mitochondria. J Proteome Res 9, 5705-5714 (2010).
  • Zhang, K., Chen, Y., Zhang, Z., Tao, S., Zhu, H. & Zhao, Y. Unrestrictive identification of non-phosphorylation PTMs in yeast kinases by MS and PTMap. Proteomics 10, 896-903 (2010).
  • Zhang, J., Chen, Y., Zhang, Z., Xing, G., Wysocka, J. & Zhao, Y. MS/MS/MS reveals false positive identification of histone serine methylation. J Proteome Res 9, 585-594 (2010).

 

2009

  • Chen, Y., Chen, W., Cobb, M.H. & 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 106, 761-766 (2009).
  • Zhang, K., Chen, Y., Zhang, Z. & Zhao, Y. Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software. J Proteome Res 8, 900-906 (2009).
  • Cheng, Z., Tang, Y., Chen, Y., Kim, S., Liu, H., Li, S.S., Gu, W. & Zhao, Y. Molecular characterization of propionyllysines in non-histone proteins. Mol Cell Proteomics 8, 45-52 (2009).
  • Chen, Y., Zhang, J., Xing, G. & Zhao, Y. Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra. J Proteome Res 8, 3141-3147 (2009).
  • Chen, W., Chen, Y., Xu, B.E., Juang, Y.C., Stippec, S., Zhao, Y. & Cobb, M.H. Regulation of a third conserved phosphorylation site in SGK J Biol Chem 284, 3453-3460 (2009).

 

2008

  • Tang, Y., Zhao, W., Chen, Y., Zhao, Y. & Gu, W. Acetylation is indispensable for p53 activation. Cell 133, 612-626 (2008).
  • Xing, G., Zhang, J., Chen, Y. & Zhao, Y. Identification of four novel types of in vitro protein modifications. J Proteome Res 7, 4603-4608 (2008).
  • Sprung, R., Chen, Y., Zhang, K., Cheng, D., Zhang, T., Peng, J. & Zhao, Y. Identification and validation of eukaryotic aspartate and glutamate methylation in proteins. J Proteome Res 7, 1001-1006 (2008).
  • Jung, S.Y., Li, Y., Wang, Y., Chen, Y., Zhao, Y. & 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 80, 1721-1729 (2008).

 

2007

  • Chen, Y., Sprung, R., Tang, Y., Ball, H., Sangras, B., Kim, S.C., Falck, J.R., Peng, J., Gu, W. & Zhao, Y. Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics 6, 812-819 (2007).
  • Chang, B., Chen, Y., Zhao, Y. & Bruick, R.K. JMJD6 is a histone arginine demethylase. Science 318, 444-447 (2007).
  • Lee, J., Xu, Y., Chen, Y., Sprung, R., Kim, S.C., Xie, S. & Zhao, Y. Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS. Mol Cell Proteomics 6, 669-676 (2007).
  • Kang, J., Chen, Y., Zhao, Y. & Yu, H. Autophosphorylation-dependent activation of human Mps1 is required for the spindle checkpoint. Proc Natl Acad Sci U S A 104, 20232-20237 (2007).
  • Ganesan, A.K., Kho, Y., Kim, S.C., Chen, Y., Zhao, Y. & White, M.A. Broad spectrum identification of SUMO substrates in melanoma cells. Proteomics 7, 2216-2221 (2007).
  • Bartz, R., Zehmer, J.K., Zhu, M., Chen, Y., Serrero, G., Zhao, Y. & Liu, P. Dynamic activity of lipid droplets: protein phosphorylation and GTP-mediated protein translocation. J Proteome Res 6, 3256-3265 (2007).

 

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. & Zhao, Y. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 23, 607-618 (2006).
  • Qiu, Y., Zhao, Y., Becker, M., John, S., Parekh, B.S., Huang, S., Hendarwanto, A., Martinez, E.D., Chen, Y., Lu, H., Adkins, N.L., Stavreva, D.A., Wiench, M., Georgel, P.T., Schiltz, R.L. & Hager, G.L. HDAC1 acetylation is linked to progressive modulation of steroid receptor-induced gene transcription. Mol Cell 22, 669-679 (2006).
  • Kim, S.C., Chen, Y., Mirza, S., Xu, Y., Lee, J., Liu, P. & Zhao, Y. A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea. J Proteome Res 5, 3446-3452 (2006).
  • Binns, D., Januszewski, T., Chen, Y., Hill, J., Markin, V.S., Zhao, Y., Gilpin, C., Chapman, K.D., Anderson, R.G. & Goodman, J.M. An intimate collaboration between peroxisomes and lipid bodies. J Cell Biol 173, 719-731 (2006).

 

2005

  • Chen, Y., Kwon, S.W., Kim, S.C. & Zhao, Y. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J Proteome Res 4, 998-1005 (2005).
  • Zhi, G., Ryder, J.W., Huang, J., Ding, P., Chen, Y., Zhao, Y., Kamm, K.E. & Stull, J.T. Myosin light chain kinase and myosin phosphorylation effect frequency-dependent potentiation of skeletal muscle contraction. Proc Natl Acad Sci U S A 102, 17519-17524 (2005).
  • Sprung, R., Nandi, A., Chen, Y., Kim, S.C., Barma, D., Falck, J.R. & Zhao, Y. Tagging-via-substrate strategy for probing O-GlcNAc modified proteins. J Proteome Res 4, 950-957 (2005).
  • Chen, Y., Kim, S.C. & Zhao, Y. High-throughput identification of in-gel digested proteins by rapid, isocratic HPLC/MS/MS. Anal Chem 77, 8179-8184 (2005).

 

2004

  • Geiman, T.M., Sankpal, U.T., Robertson, A.K., Chen, Y., Mazumdar, M., Heale, J.T., Schmiesing, J.A., Kim, W., Yokomori, K., Zhao, Y. & Robertson, K.D. Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery. Nucleic Acids Res 32, 2716-2729 (2004).