Publications | Chen Lab

2025

Ouyang H, How CY, Wang X, Yu C, Luo A, Huang L#, Chen Y#. “Crosslinking-mediated Interactome Analysis Identified PHD2-HIF1α Interaction Hotspots and the Role of PHD2 in Regulating Protein Neddylation” (under review, Cell Reports) bioRxiv [Preprint] doi: 10.1101/2024.12.16.628769.

Wei Y, Li X, Gong Y, Li Y-X, Guan J, Yuan B, Chen Y, Pang H-B. “Peroxidase-catalyzed proximity labeling to survey the proteome of nanomaterial-cell interface during macropinocytosis-mediated internalization” Nano Today Dec:65:10.1016/j.nantod.2025.102865 (2025)

Sin YC, Abernathy B, Yuan Z, Gonzalez JE, Heier J, Parker L, Mashek DG#, Chen Y#. “Sorbate Induces Lysine Sorbylation Through Non-Canonical Activities of Class I HDACs to Regulate the Expression of Inflammation Genes”, Science Advances 11, eadv1071 (2025).

Alhamdan F, Maisat W, Higgins L, Chen Y, Ibla JC, Yuki K. "The role of extracellular vesicles miRNAs in postoperative organ dysfunction in neonates and infants undergoing congenital cardiac surgery: A exploratory study", Int J Mol Sci, 26(8):3837 (2025).

Sin YC, Hosny N, Batti Angulski AB, Kim DH, Metzger JM, Chen Y "Isotopic labeling-enabled Chemical Proteomic Analysis Revealed Structural and Functional Features of Allysine Modifications in Mammalian Cells and Tissues", Analytical Chemistry, 97(18):9944-9952 (2025).

Chen Y, Gong Y “Ubiquitin E3 Ligase Activity Profiling Analysis with Quantitative Proteomics”, Methods in Molecular Biology, "Activity-Based Proteomics" Zhipeng (Toby) Tao (Eds) 2921:345-359 (2025).

Zhang D, Gao J, Zhu Z, Mao Q, Xu Z, Singh PK, Rimayi CC, Moreno-Yruela C, Xu S, Li G, Sin YC, Chen Y, Olsen CA, Snyder NW, Dai L, Li L, Zhao Y. “Lysine L-lactylation is the dominant lactylation isomer induced by glycolysis”, Nat Chem Biol. (1):91-99 (2025).

2024

Maisat W, Hou L, Sandhu S, Sin YC, Kim S, Van Pelt H, Chen Y, Emani S, Kong SW, Emani S, Ibla J, Yuki K. Neutrophil extracellular traps formation is associated with postoperative complications in congenital cardiac surgery. Pediatr Res. doi: 10.1038/s41390-024-03717-z (2024).

Sin YC, Park M, Griffin TJ, Yong J#, Chen Y#. “A constitutional isomer selective chemical proteomic strategy for system-wide profiling of protein lysine 5-hydroxylation”, Chem Sci. 15(44):18395-404 (2024).

Sun J, Kim JY, Jun S, Park M, de Jong E, Chang JW, Cheng S, Fan D, Chen Y, Griffin TJ, Lee JH, You HJ, Zhang W, Yong J. “Dichotomous intronic polyadenylation profiles reveal multifaceted gene functions in the pan-cancer transcriptome”, Exp Mol Med. (10):2145-2161 (2024).

Windsor P, Ouyang H, G da Costa JA, Rama Damodaran A#, Chen Y#, Bhagi-Damodaran A# “Gas Tunnel Engineering of Prolyl Hydroxylase Reprograms Hypoxia Signaling in Cells”, Angew Chem Int Ed Engl. 63(48):e202409234 (2024).

Rivard RS, Chang YC, Ragland RL, Thu YM, Kassab M, Mandal RS, Van Riper SK, Kulej K, Higgins L, Markowski TM, Shang D, Hedberg J, Erber L, Garcia B, Chen Y, Bielinsky AK, Brown EJ. “Improved detection of DNA replication fork-associated proteins”, Cell Rep. 43(5):114178 (2024).

Hou L, Sin YC, Chen Y, Yuki K. “Integrin CD11c regulates B cell homeostasis” Front Immunol. 15:1359608 (2024).

2023

Chen, Y., Ge, Y., Han, X., Hao, L., Huan, T., Li, L., Li, L., Li, W., … and Huang, L. “Meeting Report on the 2nd Chinese American Society for Mass Spectrometry (CASMS) Conference Advancing Biological and Pharmaceutical Mass Spectrometry” Mol. Cell. Proteomics 22(6):100559 (2023)

Nelson, S.L., Li, Y., Chen, Y. and Deshmukh, L. “Avidity-based method for the efficient generation of monoubiquitinated recombinant proteins.” Journal of the American Chemical Society 145(14):7748-7752 (2023).

Gao, J., Sheng, X., Du, J., Zhang, D., Han, C., Chen, Y., Wang, C. and Zhao, Y. “Identification of 113 new histone marks by CHiMA, a tailored database search strategy” Science Advances 9, eadf1416 (2023).

2022

Shibamura-Fujiogi, M., Wang, X., Maisat, W., Koutsogiannaki, S., Li, Y., Chen, Y., Lee, J.C. and Yuki, K. " GltS regulates biofilm formation in methicillin-resistant Staphylococcus aureus" Communications Biology 5, 1284 (2022).

Hou, L., Voit, R.A., Shibamura-Fujiogi, A., Koutsogiannaki, S., Li, Y., Chen, Y., Luo, H., Sankaran, V.G. and Yuki, K. "CD11c regulates neutrophil maturation" Blood Advances (in press).

Gong, Y., Behera, G., Erber, L., Luo, A. and Chen, Y. "HypDB: A Functionally Annotated Web-based Database of the Proline Hydroxylation Proteome" PLoS Biology 20(8): e3001757 (2022).

Gong, Y., Chen, Y. UbE3-APA: A Bioinformatic Strategy to Elucidate Ubiquitin E3 Ligase Activities in Quantitative Proteomics Study. Bioinformatics 38 (8): 2211-2218 (2022).

Erber, L., Liu, S., Gong, Y., Tran, P., Chen, Y. Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells. Molecules 27(2) (2022).

2020

Wu, Z. L., Luo, A., Grill, A., Lao, T., Zou, Y., Chen, Y. Fluorescent Detection of O-GlcNAc via Tandem Glycan Labeling. Bioconjug Chem 31(9): 2098-2102 (2020).

Luo, A., Gong, Y., Kim, H., Chen, Y. Proteome dynamics analysis identifies functional roles of SDE2 and hypoxia in DNA damage response in prostate cancer cells. NAR Cancer. 2(2): zcaa010 (2020).

Seiler, C.L., Song, J.M., Kotandeniya, D., Chen, J., Kono, T.J.Y., Han, Q., Colwell, M., Auch, B., Sarver, A.L., Upadhyaya, P., Ren, Y., Faulk, C., De Flora, S., La Maestra, S., Chen, Y., Kassie, F., Tretyakova, N.Y. Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung. Scientific Reports. 10(1): 11290 (2020).

Wang, X., Hennig, T., Whisnant, A.W., Erhard, F., Friedel, C.C., Forouzmand, E., Hu, W., Erber, L., Chen, Y., Sandri-Goldin, R., Dölken, L., Shi, Y. Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27. Nature Communications. 11, 293 (2020).

Luo, A., Chen, Y. Label-Free Interactome Analysis Revealed an Essential Role of CUL3-KEAP1 Complex in Mediating the Ubiquitination and Degradation of PHD2. J. Proteome Res. 19, 260-268 (2020).

Hauck, A. K., Zhou, T., Upadhyay, A., Sun, Y., O'Connor, M. B., Chen, Y., Bernlohr, D. A. Histone Carbonylation Is a Redox-Regulated Epigenomic Mark That Accumulates with Obesity and Aging. Antioxidants (Basel) 9(12) (2020).

2019

Chang, J.W., Yeh, H.S., Park, M., Erber, L., Sun, J., Cheng, S., Bui, A.M., Fahmi, N.A., Nasti, R., Kuang, R., Chen, Y., Zhang, W., Yong, J. mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control. Nucleic Acids Res. 47(19):10373-10387 (2019).

Chen, Y. and Li, Y. Site-specific Determination of Lysine Acetylation Stoichiometries on the Proteome-Scale. Methods Enzymology, Benjamin Garcia (Eds). 626:115-132 (2019).

Erber, L., Luo, A. and Chen, Y. Targeted and Interactome Proteomics Revealed the Role of PHD2 in Regulating BRD4 Proline Hydroxylation. Mol. Cell. Proteomics 18(9):1772-1781 (2019).

Seiler, C.L., Song, J.M., Fernandez, J., Abrahante, J.E., Kono, T., Chen, Y., Ren, Y., Kassie, F. and Tretyakova, N.Y. Epigenetic Changes in Alveolar Type II Lung Cells of A/J Mice Following Intranasal Treatment with Lipopolysaccharide. Chem Res Toxicol. 32(5): 831-839 (2019).

Li, Y., Evers, J., Luo, A., Erber, L., Postler, Z. and Chen, Y. A Quantitative Chemical Proteomics Approach for Site-specific Stoichiometry Analysis of Ubiquitination. Angew Chem Int Ed Engl. 58(2):537-541 (2019)

2018

Hauck, A.K., Zhou, T., Hahn, W., Petegrosso, R., Kaung, R., Chen, Y. and Bernlohr, D.A. Obesity-Induced Protein Carbonylation In Murine Adipose Tissue Regulates The DNA Binding Domain Of Nuclear Zinc-Finger Proteins. J. Biol. Chem. 293(35):13464-13476 (2018)

Smestad J, Erber L, Chen Y and Maher LJ. Chromatin Succinylation Correlates with Active Gene Expression and Is Perturbed by Defective TCA Cycle Metabolism. iScience 2:63-75 (2018)

Smestad J, Hamidi O, Wang L, Holte MN, Khazal FA, Erber L, Chen Y and Maher LJ. Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma. Oncotarget 9:6109-6127 (2018)

Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y and Hochedlinger K. Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling. Cell 172(1-2):106-120 (2018)

2016

Zhou, T., Erber, L., Liu, B., Gao, Y., Ruan, H.B. & Chen, Y. Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells. Oncotarget 7, 79154-79169 (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)

Chen, Y. Quantitative Analysis of the Sirt5-Regulated Lysine Succinylation Proteome in Mammalian Cells. Methods Molecular Biology, Vol. 1410, Salvatore Sechi (Eds.) (2016)

Wang, S., Li, D., Ou, Y., Jiang, L., Chen, Y., Zhao, Y., Gu, W., Acetylation Is Crucial for p53-Mediated Ferroptosis and Tumor Suppression. Cell Reports 17(2): 366-373 (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)

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. Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation. Mol. Cell 62(2):194-206 (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)

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 Biol10, 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).

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).