Yingming Zhao, Ph.D.

Link to publications page: CLICK HERE

 

2017

Lombard, D.B., Zhao, Y. ACSF3 and Mal(onate)-Adapted Mitochondria. Cell Chem. Biol., 24, 649-650.

Huang, J., Luo, Z., Ying, W., Cao, Q., Huang, H., Dong, J., Wu, Q., Zhao, Y., Qian, X., Dai, J. 2-Hydroxyisobutyrylation on histone H4K8 is regulated by glucose homeostasis in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A., 114, 8782-8787.

Liu, X., Wei, W., Liu, Y., Yang, X., Wu, J., Zhang, Y., Zhang, Q., Shi, T., Du, J.X., Zhao, Y., Lei, M., Zhou, J.Q., Li, J., Wong, J. MOF as an evolutionarily conserved histone crotonyltransferase and transcriptional activation by histone acetyltransferase-deficient and crotonyltransferase-competent CBP/p300. Cell Discovery, 3, 17016.

Lee, P., Jiang, S., Li, Y., Yue, J., Gou, X., Chen, S.Y., Zhao, Y., Schober, M., Tan, M., Wu, X. Phosphorylation of Pkp1 by RIPK4 regulates epidermal differentiation and skin tumorigenesis. EMBO J., 36, 1963-1980.

Nie, L., Shuai, L., Zhu, M., Liu, P., Xie, Z.F., Jiang, S., Jiang, H.W., Li, J., Zhao, Y., Li, J.Y., Tan, M. The Landscape of Histone Modifications in a High-Fat Diet-Induced Obese (DIO) Mouse Model. Mol. Cell. Proteomics, 16, 1324-1334.

 

2016

Sabari, B.R., Zhang, D., Allis, C.D., Zhao, Y., 2016. Metabolic regulation of gene expression through histone acylations. Nat. Rev. Mol. Cell Biol. doi:10.1038/nrm.2016.140

Xie, Z., Zhang, D., Chung, D., Tang, Z., Huang, H., Dai, L., Qi, S., Li, J., Colak, G., Chen, Y., Xia, C., Peng, C., Ruan, H., Kirkey, M., Wang, D., Jensen, L.M., Kwon, O.K., Lee, S., Pletcher, S.D., Tan, M., Lombard, D.B., White, K.P., Zhao, H., Li, J., Roeder, R.G., Yang, X., Zhao, Y., 2016. Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation. Mol. Cell 62,194–206.doi:10.1016/j.molcel.2016.03.036

Goudarzi, A., Zhang, D., Huang, H., Barral, S., Kwon, O.K., Qi, S., Tang, Z., Buchou, T., Vitte, A L., He, T., Cheng, Z., Montellier, E., Gaucher, J., Curtet, S., Debernardi, A., Charbonnier, G., Puthier, D., Petosa, C., Panne, D., Rousseaux, S., Roeder, R.G., Zhao, Y**., Khochbin, S** (co-corresponding author., 2016. Dynamic Competing Histone H4 K5K8 Acetylation and Butyrylation Are Hallmarks of Highly Active Gene Promoters. Mol. Cell 62, 169–180.doi:10.1016/j.molcel.2016.03.014

Li, Y., Sabari, B.R., Panchenko, T., Wen, H., Zhao, D., Guan, H., Wan, L., Huang, H., Tang, Z., Zhao, Y., Roeder, R.G., Shi, X., Allis, C.D., Li, H., 2016. Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain. Mol. Cell 62, 181–193.doi:10.1016/j.molcel.2016.03.028

Xiong, X., Panchenko, T., Yang, S., Zhao, S., Yan, P., Zhang, W., Xie, W., Li, Y., Zhao, Y., Allis, C.D., Li, H., 2016. Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2. Nat. Chem. Biol. 12, 1111–1118. doi:10.1038/nchembio.2218

Martínez-Reyes, I., Diebold, L.P., Kong, H., Schieber, M., Huang, H., Hensley, C.T., Mehta, M.M., Wang, T., Santos, J.H., Woychik, R., Dufour, E., Spelbrink, J.N., Weinberg, S.E., Zhao, Y., DeBerardinis, R.J., Chandel, N.S., 2016. TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions. Mol. Cell 61, 199–209doi:10.1016/j.molcel.2015.12.002

Kaczmarska, Z., Ortega, E., Goudarzi, A., Huang, H., Kim, S., Márquez, J.A., Zhao, Y., Khochbin, S., Panne, D., 2017. Structure of p300 in complex with acyl-CoA variants. Nat Chem Biol 13, 21–29.doi:10.1038/nchembio.2217

Respuela, P., Nikolić, M., Tan, M., Frommolt, P., Zhao, Y., Wysocka, J., Rada-Iglesias, A., 2016. Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification. Cell Stem Cell 18, 118–133. doi:10.1016/j.stem.2015.09.010

Wang, S.-J., Li, D., Ou, Y., Jiang, L., Chen, Y., Zhao, Y., Gu, W., 2016. Acetylation Is Crucial for p53-Mediated Ferroptosis and Tumor Suppression. Cell Rep 17, 366–373.doi:10.1016/j.celrep.2016.09.022

Zhao, D., Guan, H., Zhao, S., Mi, W., Wen, H., Li, Y., Zhao, Y., Allis, C.D., Shi, X., Li, H., 2016. YEATS2 is a selective histone crotonylation reader. Cell Res 26, 629–632.doi:10.1038/cr.2016.49

Liu, K., Li, F., Han, H., Chen, Y., Mao, Z., Luo, J., Zhao, Y., Zheng, B., Gu, W., Zhao, W., 2016. Parkin Regulates the Activity of Pyruvate Kinase M2. J. Biol. Chem. 291, 10307–10317.doi:10.1074/jbc.M115.703066

Washburn, M.P., Zhao, Y., Garcia, B.A., 2016. Reshaping the Chromatin and Epigenetic Landscapes with Quantitative Mass Spectrometry. Mol. Cell Proteomics 15, 753–754.doi:10.1074/mcp.E116.058602

Aramsangtienchai, P., Spiegelman, N.A., He, B., Miller, S.P., Dai, L., Zhao, Y., Lin, H., 2016. HDAC8 Catalyzes the Hydrolysis of Long Chain Fatty Acyl Lysine. ACS Chem. Biol. 11, 2685 2692. doi:10.1021/acschembio.6b00396

Qian, L., Nie, L., Chen, M., Liu, P., Zhu, J., Zhai, L., Tao, S., Cheng, Z., Zhao, Y., Tan, M., 2016. Global Profiling of Protein Lysine Malonylation in Escherichia coli Reveals Its Role in Energy Metabolism. J. Proteome Res. 15, 2060–2071. doi:10.1021/acs.jproteome.6b00264

Sun, M., Xu, J., Wu, Z., Zhai, L., Liu, C., Cheng, Z., Xu, G., Tao, S., Ye, B.-C., Zhao, Y., Tan, M., 2016. Characterization of Protein Lysine Propionylation in Escherichia coli: Global Profiling, Dynamic Change, and Enzymatic Regulation. J. Proteome Res. 15, 4696–4708.doi:10.1021/acs.jproteome.6b00798

Morozumi, Y., Boussouar, F., Tan, M., Chaikuad, A., Jamshidikia, M., Colak, G., He, H., Nie, L., Petosa, C., de Dieuleveult, M., Curtet, S., Vitte, A.-L., Rabatel, C., Debernardi, A., Cosset, F.-L., Verhoeyen, E., Emadali, A., Schweifer, N., Gianni, D., Gut, M., Guardiola, P., Rousseaux, S., Gérard, M., Knapp, S., Zhao, Y., Khochbin, S., 2016. Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells. J Mol Cell Biol 8, 349–362. doi:10.1093/jmcb/mjv060

Kwon, O.K., Kim, S.J., Lee, Y.-M., Lee, Y.-H., Bae, Y.-S., Kim, J.Y., Peng, X., Cheng, Z., Zhao, Y., Lee, S., 2016. Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio). Proteomics 16, 136–149. doi:10.1002/pmic.201500017

2015

Huang H, Lin S, Garcia BA, Zhao Y, Quantitative Proteomic Analysis of Histone Modifications. Chem Rev. 2015 Mar 25;115(6):2376-418. doi: 10.1021/cr500491u.

Colak G, Pougovkina O, Dai L, Tan M, Te Brinke H, Huang H, Cheng Z, Park J, Wan X, Liu X, Yue WW, Wanders RJ, Locasale JW, Lombard DB, de Boer VC, Zhao Y, Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation. Mol Cell Proteomics. 2015 Nov;14(11):3056-71. doi: 10.1074/mcp.M115.048850. Epub 2015 Aug 28.

Hirschey MD, Zhao Y, Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation. Mol Cell Proteomics. 2015 Sep;14(9):2308-15.

Wu Z, Cheng Z, Sun M, Wan X, Liu P, He T, Tan M, Zhao Y, A chemical proteomics approach for global analysis of lysine monomethylome profiling. Mol Cell Proteomics. 2015 Feb;14(2):329-39. doi: 10.1074/mcp.M114.044255.

Zhao Y, Garcia BA, Comprehensive Catalog of Currently Documented Histone Modifications. Cold Spring Harb Perspect Biol. 2015 Sep 1;7(9):a025064. doi: 10.1101/cshperspect.a025064.

Kang Y, Zhou XE, Gao X, He Y, Liu W, Ishchenko A, Barty A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Ke J, Tan MH, Zhang C, Moeller A, West GM, Pascal BD, Van Eps N, Caro LN, Vishnivetskiy SA, Lee RJ, Suino-Powell KM, Gu X, Pal K, Ma J, Zhi X, Boutet S, Williams GJ, Messerschmidt M, Gati C, Zatsepin NA, Wang D, James D, Basu S, Roy-Chowdhury S, Conrad CE, Coe J, Liu H, Lisova S, Kupitz C, Grotjohann I, Fromme R, Jiang Y, Tan M, Yang H, Li J, Wang M, Zheng Z, Li D, Howe N, Zhao Y, Standfuss J, Diederichs K, Dong Y, Potter CS, Carragher B, Caffrey M, Jiang H, Chapman HN, Spence JC, Fromme P, Weierstall U, Ernst OP, Katritch V, Gurevich VV, Griffin PR, Hubbell WL, Stevens RC, Cherezov V, Melcher K, Xu HE, Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature. 2015 Jul 30;523(7562):561-7. doi: 10.1038/nature14656. Epub 2015 Jul 22.

Sabari BR, Tang Z, Huang H, Yong-Gonzalez V, Molina H, Kong HE, Dai L, Shimada M, Cross JR, Zhao Y, Roeder RG, Allis CD, Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol Cell. 2015 Apr 16;58(2):203-15. doi: 10.1016/j.molcel.2015.02.029. Epub 2015 Mar 26.

Head SA, Shi W, Zhao L, Gorshkov K, Pasunooti K, Chen Y, Deng Z, Li RJ, Shim JS, Tan W, Hartung T, Zhang J, Zhao Y, Colombini M, Liu JO. Antifungal drug itraconazole targets VDAC1 to modulate the AMPK/mTOR signaling axis in endothelial cells. Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):E7276-85. doi: 10.1073/pnas.1512867112.

He QL, Titov DV, Li J, Tan M, Ye Z, Zhao Y, Romo D, Liu JO, Covalent Modification of a Cysteine Residue in the XPB Subunit of the General Transcription Factor TFIIH Through Single Epoxide Cleavage of the Transcription Inhibitor Triptolide. Angew Chem Int Ed Engl. 2015 Feb 2;54(6):1859-63. doi: 10.1002/anie.201408817.

Torres MJ, Pandita RK, Kulak O, Kumar R, Formstecher E, Horikoshi N, Mujoo K, Hunt CR, Zhao Y, Lum L, Zaman A, Yeaman C, White MA, Pandita TK, Role of the Exocyst Complex Component Sec6/8 in Genomic Stability. Mol Cell Biol. 2015 Nov 1;35(21):3633-45. doi: 10.1128/MCB.00768-15. Epub 2015 Aug 17.

Morozumi Y, Boussouar F, Tan M, Chaikuad A, Jamshidikia M, Colak G, He H, Nie L, Petosa C, de Dieuleveult M, Curtet S, Vitte AL, Rabatel C, Debernardi A, Cosset FL, Verhoeyen E, Emadali A, Schweifer N, Gianni D, Gut M, Guardiola P, Rousseaux S, Gérard M, Knapp S, Zhao Y, Khochbin S. Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells. J Mol Cell Biol. 2015 Oct 12. pii: mjv060.

Liu H, Yue J, Huang H, Gou X, Chen SY, Zhao Y, Wu X. Regulation of Focal Adhesion Dynamics and Cell Motility by EB2 and Hax1 Complex. J Biol Chem. 2015 Nov 2. pii: jbc.M115.671743.

Cluntun AA, Huang H, Dai L, Liu X, Zhao Y, Locasale JW. The rate of glycolysis quantitatively mediates specific histone acetylation sites. Cancer Metab. 2015 Sep 23;3:10. doi: 10.1186/s40170-015-0135-3. eCollection 2015.

Kwon OK, Kim S, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S. Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio). Proteomics. 2015 Oct 9. doi: 10.1002/pmic.201500017.

2014

Huang H, Sabari BR, Garcia BA, Allis CD, Zhao Y, SnapShot: Histone Modifications. Cell. 2014 Oct 9;159(2):458-458.e1. doi: 10.1016/j.cell.2014.09.037.

Dai L, Peng C, Montellier E, Lu Z, Chen Y, Ishii H, Debernardi A, Buchou T, Rousseaux S, Jin F, Sabari BR, Deng Z, Allis CD, Ren B, Khochbin S, Zhao Y, Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat Chem Biol. 2014, doi: 10.1038/nchembio.1497.

Tan M, Peng C, Anderson KA, Chhoy P, Xie Z, Dai L, Park J, Chen Y, Huang H, Zhang Y, Ro J, Wagner GR, Green MF, Madsen AS, Schmiesing J, Peterson BS, Xu G, Ilkayeva OR, Muehlbauer MJ, Braulke T, Mühlhausen C, Backos DS, Olsen CA, McGuire PJ, Pletcher SD, Lombard DB, Hirschey MD, Zhao Y, Lysine Glutarylation Is a Protein Posttranslational Modification Regulated by SIRT5. Cell Metab. 2014, 19, 605-17.

Wu Z, Cheng Z, Sun M, Wan X, Liu P, He T, Tan M, Zhao Y, A Chemical Proteomics Approach for Global Analysis of Lysine Mono-Methylation. Mol Cell Proteomics. 2014, pii: mcp.M114.044255.

Tang S, Huang G, Fan W, Chen Y, Ward JM, Xu X, Xu Q, Kang A, McBurney MW, Fargo DC, 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. Mol Cell. 2014 Aug 20. pii: S1097-2765(14)00604-2. doi: 10.1016/j.molcel.2014.07.011.

He QL, Titov DV, Li J, Tan M, Ye Z, Zhao Y, Romo D, Liu JO, Covalent Modification of a Cysteine Residue in the XPB Subunit of the General Transcription Factor TFIIH Through Single Epoxide Cleavage of the Transcription Inhibitor Triptolide. Angew Chem Int Ed Engl. 2014, doi: 10.1002/anie.201408817.

Kazgan N, Metukuri MR, Purushotham A, Lu J, Rao A, Lee S, Pratt-Hyatt M, Lickteig A, Csanaky I, Zhao Y, Dawson PA, Li X. Intestine-specific Deletion of Sirt1 in Mice Impairs DCoH2-HNF1α-FXR Signaling and Alters Systemic Bile Acid Homeostasis. Gastroenterology, 2014, 146, 1006-16.

Xu G, Wang J, Wu Z, Qian L, Dai L, Wan X, Tan M, Zhao Y, Wu Y, SAHA regulates histone acetylation, butyrylation and protein expression in neuroblastoma. J Proteome Res. 2014, DOI: 10.1021/pr500497e

 Luo X, Wang B, Tang F, Zhang J, Zhao Y, Li H, Jin Y. Wwp2 targets SRG3, a scaffold protein of the SWI/SNF-like BAF complex, for ubiquitination and degradation. Biochem Biophys Res Commun, 2014, 443, 1048-53.

Sun H, Chen X, Yuan F, Liu J, Zhao Y, Chen SY. Involvement of seven in absentia homolog-1 in ethanol-induced apoptosis in neural crest cells. Neurotoxicol Teratol. 2014 Sep 3;46C:26-31. doi: 10.1016/j.ntt.2014.08.006.

Zhang Y, Wu Z, Wan X, Liu P, Zhang J, Ye Y, Zhao Y, Tan M, Comprehensive Profiling of Lysine Acetylome in Staphylococcus aureus. Sci China Chem. In Press.

2013

Park J, Chen Y, Tishkoff DX, Peng C, Tan M, Dai L, Xie Z, Zhang Y, Zwaans BM, Skinner ME, Lombard DB, Zhao Y, SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. Mol Cell, 2013, 50, 919-30.

Colak G, Xie Z, Zhu AY, Dai L, Lu Z, Zhang Y, Wan X, Chen Y, Cha YH, Lin H, Zhao Y, Tan M. Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. Mol Cell Proteomics, 2013, 12, 3509-20.

Chen Y, Colak G, Zhao Y, SILAC-Based Quantification of Sirt1-Responsive Lysine Acetylome. Methods Mol Biol, 2013, 1077, 105-20.

Dobbin MM, Madabhushi R, Pan L, Chen Y, Kim D, Gao J, Ahanonu B, Pao PC, Qiu Y, Zhao Y, Tsai LH, SIRT1 collaborates with ATM and HDAC1 to maintain genomic stability in neurons. Nat Neurosci, 2013, 16, 1008-15.

Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S, Recombinant antibodies to histone post-translational modifications. Nat Methods, 2013, 18. doi: 10.1038/nmeth.2605.

Montellier E, Boussouar F, Rousseaux S, Zhang K, Buchou T, Fenaille F, Shiota H, Debernardi A, Héry P, Curtet S, Jamshidikia M, Barral S, Holota H, Bergon A, Lopez F, Guardiola P, Pernet K, Imbert J, Petosa C, Tan M, Zhao Y, Gérard M, Khochbin S., Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B. Genes Dev, 2013, 27, 1680-92.

Lee S, Tan M, Dai L, Kwon OK, Yang JS, Zhao Y, Chen Y, MS/MS of synthetic peptide is not sufficient to confirm new types of protein modifications. J Proteome Res, 2013, 12, 1007-13.

 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, 2013, 228, 1443-51.

 

2012

Xie, Z., Dai, J., Dai, L., Tan, M., Cheng, Z., Wu,Y., Boeke, J. D., Zhao, Y., Lysine succinylation and lysine malonylation in histones. Mol Cell Proteomics, 2012, 11, 100-7. 

Chen, Y., Zhao, W., Yang, J.S., Cheng, Z., Luo, H., Lu, Z., Tan, M., Gu, W., and Zhao, Y., Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways. Mol Cell Proteomics, 2012, 11, 1048-62.

Li, N., Kon, N., JIang, L., Tan, M., Ludwig, T., Zhao, Y., Baer, R., W., G., Tumor suppression in the absence of p53-mediated cell cycle arrest, apoptosis, and senescence. Cell, 149, 1269-83

Qiang, L., Wang, L., Kon, N., Lee, S., Zhao, Y., Gu, W., Farmer, S.R., Accili, D., Brown remodeling of white adipocytes by SirT1-dependent deacetylation of PPARγ. Cell, 2012, 150, 620-32.

Choi, M.C., Cohen, T.J., Barrientos, T., Wang, B., Simmons, B.J., Li, M., Yang, J.S., Cox, G.A., Zhao, Y., Yao, T.P., A direct HDAC4-MAP kinase crosstalk activates neurogenic muscle atrophy. Mol Cell, 2012, 47, 1-11.

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, 191-6.

Montellier, E., Rousseaux, S., Zhao, Y., Khochbin S. Histone crotonylation specifically marks the haploid male germ cell gene expression program. Bioessays, 2012, 34, 187-93.

 

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, 1016-28.

Zhang, Z., Tan, M., Xie, Z., Dai, L., Chen, Y., and Zhao, Y., Identification of lysine   succinylation as a new post-translational modification. Nat Chem Biol, 2011, 7, 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, 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, 969-979.

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, 23831-41.

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, 5567-77.

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., Shen, J., Luther, G., Hu, N., Zhou, Q., Luu, H.H., Haydon, R.C., Zhao, Y., He, T.C.,  Tetrandrine Inhibits Wnt/b-Catenin Signaling and Suppresses Tumor Growth of Human Colorectal Cancer. Mol Pharmacol2011, 79, 211-9.

Chu,C., Hou, H., Zhang, J., Phu, L., Loktev, A.V.,  Kirkpatrick, D.S.,  Jackson, P.J., Zhao, Y., Zou, H., A novel acetylation of β-tubulin by San modulates microtubule polymerization via down-regulating tubulin incorporation, Mol Biol Cell, 2011, 22, 448-56.

Lu, Z., Cheng, Z., Zhao, Y., Volchenboum ,S.L., Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. PLoS One, 2011, 6, 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, e17153.

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. Biochem Biophys Res Commun, 2011, 404, 68–73.

 

2010

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, 585-94.

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

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, 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, ra9.

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. PMCID: PMC2824367

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, 935-47.

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, 25161-7.

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, 896-903.

 

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, 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, 45-52.

Zhang, J., Sprung, R., Pei, J., Tan, X., Kim, S., Zhu, H., Liu, C.F., Grishin, N.V., Zhao, Y., Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics, 2009, 8, 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, 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, 1290-302.

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, e1000235.

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, 13785-90.

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, 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, 3141-7.

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

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

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, 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, 3453-60.

 

2008

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

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, 2008, 7, 1001-6.

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

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, 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, 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, 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, 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 Cell Proteomics, 2007, 6, 669-76.

Chang, B., Chen, Y., Zhao, Y. and Bruick, R.K., JMJD6 is a histone arginine demethylase. Science, 2007, 318, 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, 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, 2005-14.

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, 1153-7.

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, 3256-65.

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, 5296-305.

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, 2007, 7, 2216-21.

 

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, 607-18.

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, 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, 669-679.

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

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

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, 3446-52.

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, 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, 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, 719-31.

 

2005

Sprung R, Nandi A, Chen Y, Kim SC, Barma D, Falck JR, Zhao Y. Tagging-via-substrate strategy for probing O-GlcNAc modified proteins. J Proteome Res, 2005, 4, 950-7.

Chen Y, Kwon SW, Kim SC, Zhao Y. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J Proteome Res. 2005, 4, 998-1005.

Cheng J, Zhang D, Kim K, Zhao Y, Zhao Y, Su B. Mip1, an MEKK2-interacting protein, controls MEKK2 dimerization and activation. Mol Cell Biol, 2005, 25, 5955-64.

Zhou G, Li H, Gong Y, Zhao Y, Cheng J, Lee P, Zhao Y. Proteomic analysis of global alteration of protein expression in squamous cell carcinoma of the esophagus. Proteomics, 2005, 5, 3814-21.

 

2004

Kho Y, Kim SC, Jiang C, Barma D, Kwon SW, Cheng J, Jaunbergs J, Weinbaum C, Tamanoi F, Falck J, Zhao Y. A tagging-via-substrate technology for detection and proteomics of farnesylated proteins. Proc Natl Acad Sci U S A, 2004, 101, 12479-84.

Zhao Y, Kwon SW, Anselmo A, Kaur K, White MA. Broad spectrum identification of cellular small ubiquitin-related modifier (SUMO) substrate proteins. J Biol Chem, 2004, 279, 20999-1002.

Zhao Y, Zhang W, Kho Y, Zhao Y. Proteomic analysis of integral plasma membrane proteins. Anal Chem. 2004, 76, 1817-23.

Geiman TM, Sankpal UT, Robertson AK, Chen Y, Mazumdar M, Heale JT, Schmiesing JA, Kim W, Yokomori K, Zhao Y, Robertson KD. Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery. Nucleic Acids Res, 2004, 32, 2716-29.

Liu P, Ying Y, Zhao Y, Mundy DI, Zhu M, Anderson RG. Chinese hamster ovary K2 cell lipid droplets appear to be metabolic organelles involved in membrane traffic. J Biol Chem, 2004, 279, 3787-92. 

Leak LV, Liotta LA, Krutzsch H, Jones M, Fusaro VA, Ross SJ, Zhao Y, Petricoin EF 3rd, Proteomic analysis of lymph. Proteomics. 2004, 4, 753-65. 

Berman DM, Shih IeM, Burke LA, Veenstra TD, Zhao Y, Conrads TP, Kwon SW, Hoang V, Yu LR, Zhou M, Kurman RJ, Petricoin EF, Liotta LA. Profiling the activity of G proteins in patient-derived tissues by rapid affinity-capture of signal transduction proteins (GRASP). Proteomics, 2004, 4, 812-8.

Geiman TM, Sankpal UT, Robertson AK, Zhao Y, Zhao Y, Robertson KD. DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system. Biochem Biophys Res Commun, 2004, 318, 544-55.