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Xiaobing Shi, Ph.D.

Present Title & Affiliation

Primary Appointment

Assistant Professor, Department of Biochemistry and Molecular Biology, Division of Basic Science Research, The University of Texas M. D. Anderson Cancer Center, Houston, TX

Research Interests


We are interested in epigenetic regulation of gene expression during development and in pathogenesis of cancers and other human diseases.  Epigenetics is termed as heritable changes in phenotype or gene expression caused by mechanisms other than changes in the underlying DNA sequence.  One of the mechanisms is through covalent modifications, including methylation, of histones, the basic proteins wound by DNA to form chromatin in the eukaryotic cells.  Histone methylation is dynamically regulated by enzymes that add and remove the methyl marks, which induces interactions with protein “effectors” that dictate the “on” or “off” states of the underlying genes.  Mutation or deletion of either the enzymes or the effectors for histone methylation have been involved in multiple human diseases including cancer.  Our long-term goal is to understand the molecular mechanisms of epigenetic regulation during development, and how disruption of the chromatin homeostasis leads to pathological development including cancers.  Current ongoing projects in the lab are: (1) Genome-wide identification of protein effectors that recognize distinct histone methylation using peptide microarrays.  (2) Identification and characterization of novel histone methyltransferases and novel methylation events on histones and non-histone proteins. (3) Elucidating the role of histone methylation in determining stem cell identity.

Office Address

The University of Texas M. D. Anderson Cancer Center
1515 Holcombe Blvd
Unit Number: Unit 1000
Houston, TX 77030
Room Number: BSRB, Rm. S9.8316A
Phone: 713-834-6293
Fax: 713-792-0346
Email: xbshi@mdanderson.org

Education & Training

Degree-Granting Education

2001 Shanghai Institute for Biological Sciene, Chinese Academy of Sciences, Shanghai, China, PHD, Plant Biology
1996 Wuhan University, Wuhan, China, BS, Biology

Postgraduate Training

2005-2008 Research Fellowship, Molecular and Cell Biology, Stanford University, Stanford, CA, Or Gozani
2001-2004 Research Fellowship, Biochemistry, Stanford University, Stanford, CA, Arthur Kornberg

Experience/Service

Academic Appointments

Member, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 11/2008-present

Honors and Awards

2009-present Welch Research Grant, Welch Foundation
2001 Pengyingang Award, Chinese Academy of Sciences
2000 Baoijie Award, Chinese Academy of Sciences
1996 Graduated with honors, Wuhan University

Selected Publications

Peer-Reviewed Original Research Articles
1. McCord RA, Michishita E, Hong T, Berber E, Boxer LD, Kusumoto R, Guan S, Shi X, Gozani O, Burlingame AL, Bohr VA, Chua KF. SIRT6 stabilizes DNA-dependent Protein Kinase at chromatin for DNA double-strand break repair. Aging 1(1):109-121, 1/2009.
2. Kachirskaia I, Shi X, Yamaguchi H, Tanoue K, Wen H, Wang EW, Appella E, Gozani O. Role for 53BP1 Tudor domain recognition of p53 dimethylated at lysine 382 in DNA damage signaling. J Biol Chem 283(50):34660-6, 12/12/2008. e-Pub 10/7/2008. PMCID: PMC2596381.
3. Zhang H, Gómez-García MR, Shi X, Rao NN, Kornberg A. Polyphosphate kinase 1, a conserved bacterial enzyme, in a eukaryote, Dictyostelium discoideum, with a role in cytokinesis. Proc Natl Acad Sci U S A 104(42):16486-91, 10/16/2007. e-Pub 10/10/2007. PMCID: PMC2034253.
4. Shi X, Kachirskaia I, Yamaguchi H, West LE, Wen H, Wang EW, Dutta S, Appella E, Gozani O. Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol Cell 27(4):636-46, 8/17/2007. PMID: 17707234.
5. Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi X, Gozani O, Cheng X, Shi Y. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448(7154):718-22, 8/9/2007. PMID: 17687328.
6. Huang W, Zhang H, Davrazou F, Kutateladze TG, Shi X, Gozani O, Prestwich GD. Stabilized phosphatidylinositol-5-phosphate analogues as ligands for the nuclear protein ING2: chemistry, biology, and molecular modeling. J Am Chem Soc 129(20):6498-506, 5/23/2007. e-Pub 5/1/2007. PMCID: PMC2553394.
7. Shi X, Kachirskaia I, Walter KL, Kuo JH, Lake A, Davrazou F, Chan SM, Martin DG, Fingerman IM, Briggs SD, Howe L, Utz PJ, Kutateladze TG, Lugovskoy AA, Bedford MT, Gozani O. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J Biol Chem 282(4):2450-5, 1/26/2007. e-Pub 12/1/2006. PMID: 17142463.
8. Martin DG, Baetz K, Shi X, Walter KL, MacDonald VE, Wlodarski MJ, Gozani O, Hieter P, Howe L. The Yng1p plant homeodomain finger is a methyl-histone binding module that recognizes lysine 4-methylated histone H3. Mol Cell Biol 26(21):7871-9, 11/2006. e-Pub 8/21/2006. PMCID: PMC1636756.
9. Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, Carney D, Peña P, Lan F, Kaadige MR, Lacoste N, Cayrou C, Davrazou F, Saha A, Cairns BR, Ayer DE, Kutateladze TG, Shi Y, Côté J, Chua KF, Gozani O. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442(7098). e-Pub 5/21/2006. PMID: 16728974.
10. Peña PV, Davrazou F, Shi X, Walter KL, Verkhusha VV, Gozani O, Zhao R, Kutateladze TG. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442(7098). e-Pub 5/21/2006. PMID: 16728977.
11. Shi X, Kornberg A. Endopolyphosphatase in Saccharomyces cerevisiae undergoes post-translational activations to produce short-chain polyphosphates. FEBS Lett 579(9):2014-8, 3/28/2005. PMID: 15792812.
12. Shi X, Rao NN, Kornberg A. Inorganic polyphosphate in Bacillus cereus: motility, biofilm formation, and sporulation. Proc Natl Acad Sci U S A 101(49):17061-5, 12/7/2004. e-Pub 11/30/2004. PMCID: PMC535361.
13. Ni Z, Shi X and Wei JM. Functional consequences of N- or C-terminal deletions of the delta subunit of chloroplast ATP synthase. Biochemistry, 2004.
14. Shi X, Wei JM and Shen Y. Sequential deletions from the N terminus or C terminus of epsilon subunit of the chloroplast ATP synthase. Biochemistry 40:10825-10831, 2001.

Invited Articles
1. Shi X, Gozani O. The fellowships of the INGs. J Cell Biochem 96(6):1127-36, 12/2005. PMID: 16167330.

Last updated: 7/2/2009