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Publications

2014

Wen H*, Li Y*, Xi Y*, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W*, Li H*, Shi X* (2014) ZMYND11 links histone H3.3 K36 trimethylation to transcription elongation and tumor suppression. Nature doi:10.1038/nature13045. (*Equal contribution)

Jiang Y, Trescott L, Holcomb J, Zhang X, Brunzelle J, Sirinupong N, Shi X & Yang Z (2014) Structural Insights into Estrogen Receptor Alpha Methylation by Histone Methyltransferase SMYD2, a Cellular Event Implicated in Estrogen Signaling Regulation. J Mol Biol doi:10.1016/j.jmb.2014.02.019

Klein BJ*, Piao L*, Xi Y, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zheng X, Cortazar M, Peña PV, Mangan A, Bentley DL, Strahl BD, Groudine M, Li W, Shi X*, Kutateladze T* (2014) KDM5B demethylase binds to its histone target and the product through distinct modules. Cell Reports pii: S2211-1247(13)00766-3. doi: 10.1016 (*Equal contribution) PMID: 24412361 PMCID: PMC3918441

2013

Zhang X, Tanaka K, Yan J, Li J, Peng D, Jiang Y, Yang Z, Barton MC, Wen H, Shi X (2013) Regulation of estrogen receptor α by histone methyltransferase SMYD2-mediated protein methylation. Proc Natl Acad Sci USA 110(43):17284-9. PMID: 24101509 PMCID: PMC3808627

Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J, Bai G, Wang P, Zhang SW, Liu ZW, Cai T, Tang K, Liu R, Shi X, He XJ, Zhu JK (2013) DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci USA 110(20):8290-5. PMID: 23637343 PMCID: PMC3657815

Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carlson S, Shi X, Balaz S, Markley JL, Glass KC (2013) Molecular Insights into the Recognition of N-Terminal Histone Modifications by the BRPF1 Bromodomain. J Mol Biol PMID: 24333487

Wang J, Leung JW, Gong Z, Feng L, Shi X, Chen J (2013) PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesis. J Biol Chem 288(5):3174-83. PMID: 23229552 PMCID: PMC3561539

2012

Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K, Kan Y, La H, Li X, Li S, Zhu X, Shi X, Zhang K, Pontes O, Chen X, Liu R, Gong Z, Zhu JK (2012) A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336(6087): 1445-8. PMID: 22700931 PMCID: PMC3575687

Brien GL, Gambero G, O'Connell DJ, Jerman E, Turner SA, Egan CM, Dunne EJ, Jurgens MC, Wynne K, Piao L, Lohan AJ, Ferguson N, Shi X, Sinha KM, Loftus BJ, Cagney G, Bracken AP (2012) Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. Nat Struct Mol Biol 19(12):1273-81. PMID: 23160351

Dhar SS, Lee SH, Kan PY, Voigt P, Ma L, Shi X, Reinberg D, Lee MG (2012) Trans-tail regulation of MLL4-catalyzed H3K4 methylation by H4R3 symmetric dimethylation is mediated by a tandem PHD of MLL4. Genes Dev 26(24):2749-62. PMID: 23249737 PMCID: PMC3533079

Calnan DR, Webb AE, White JL, Stowe TR, Goswami T, Shi X, Espejo A, Bedford MT, Gozani O, Gygi SP, Brunet A (2012) Methylation by Set9 modulates FoxO3 stability and transcriptional activity. Aging (Albany NY) 4(7):462-79. PMID: 22820736 PMCID: PMC3433933

Zhang X, Wen H, Shi X (2012) Lysine methylation: beyond histones. Review. Acta Biochim Biophys Sin (Shanghai) 44(1):14-27. PMID: 22194010

2011

Kuo AJ, Cheung P, Chen K, Zee BM, Lauring J, Xi Y, Park BH, Shi X, Kioi M, Garcia BA, Li W, Gozani O (2011) NSD2 links dimethylation of histone H3K36 to oncogenic programming. Mol Cell 44(4):609-20. PMID: 22099308 PMCID: PMC3222870

Levy D, Kuo AJ, Chang Y, Schaefer U, Kitson C, Cheung P, Espejo A, Zee BM, Liu CL, Tangsombatvisit S, Tennen RI, Kuo AY, Tanjing S, Cheung R, Chua KF, Utz PJ, Shi X, Prinjha RK, Lee K, Garcia BA, Bedford MT, Tarakhovsky A, Cheng X, Gozani O (2011) Lysine methylation of the NF-kB subunit RelA by SETD6 couples activity of GLP to tonic repression of NF-kB signaling. Nat Immunol 12(1):29-36. PMID: 21131967 PMCID: PMC3074206

2010

Tsai WW, Wang Z, Yiu TT, Akdemir KC, Xia W, Winter S, Tsai CY, Shi X, Schwarzer D, Plunkett W, Aronow B, Gozani O, Fischle W, Hung MC, Patel DJ, Barton MC (2010) TRIM24 links a non-canonical histone signature to breast cancer. Nature 468(7326):927-32. PMID: 21164480 PMCID: PMC3058826

Wen H, Li J, Song T, Lu M, Kan PY, Lee MG, Sha B, Shi X (2010) Recognition of histone H3K4 trimethylation by the PHD finger of PHF2 modulates histone demethylation. J Biol Chem 285(13):9322, 2/2010. e-Pub 2/2010. PMID: 20129925 PMCID: PMC2843180

West LE, Roy S, Lachmi-Weiner K, Hayashi R, Shi X, Appella E, Kutateladze TG, Gozani O (2010) The MBT repeats of L3MBTL1 link set8 mediated p53 methylation at lysine 382 to target gene repression. J Biol Chem 285(48):37725-32. PMID: 20870725 PMCID: PMC2988377

Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M, Tommerup N, Shi X, Gozani O, Rappsilber J, Salcini AE, Helin K (2010) A Functional Link between the Histone Demethylase PHF8 and the Transcription Factor ZNF711 in X-Linked Mental Retardation. Mol Cell 38. e-Pub 3/2010. PMID: 20346720 PMCID: PMC2989439

2009 and before

McCord RA, Michishita E, Hong T, Berber E, Boxer LD, Kusumoto R, Guan S, Shi X, Gozani O, Burlingame AL, Bohr VA, Chua KF (2009) SIRT6 stabilizes DNA-dependent Protein Kinase at chromatin for DNA double-strand break repair. Aging 1(1):109-121, 1/2009. PMID: 20157594 PMCID: PMC2815768

Kachirskaia I, Shi X, Yamaguchi H, Tanoue K, Wen H, Wang EW, Appella E, Gozani O (2008) 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. PMID: 18840612 PMCID: PMC2596381

Zhang H, Gómez-García MR, Shi X, Rao NN, Kornberg A (2007) 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. PMID: 17940044 PMCID: PMC2034253

Shi X, Kachirskaia I, Yamaguchi H, West LE, Wen H, Wang EW, Dutta S, Appella E, Gozani O (2007) Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol Cell 27(4):636-46, 8/17/2007. PMID: 17707234 PMCID: PMC2693209

Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi X, Gozani O, Cheng X, Shi Y (2007) Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448(7154):718-22, 8/9/2007. PMID: 17687328 PMCID: PMC2702779

Huang W, Zhang H, Davrazou F, Kutateladze TG, Shi X, Gozani O, Prestwich GD (2007) 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. PMID: 17469822 PMCID: PMC2553394

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 (2006) 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 PMCID: PMC2735445

Martin DG, Baetz K, Shi X, Walter KL, MacDonald VE, Wlodarski MJ, Gozani O, Hieter P, Howe L (2006) 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. PMID: 16923967 PMCID: PMC1636756

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 (2006) ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442(7098). e-Pub 5/21/2006. PMID: 16728974 PMCID: PMC3089773

Peña PV, Davrazou F, Shi X, Walter KL, Verkhusha VV, Gozani O, Zhao R, Kutateladze TG (2006) Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442(7098). e-Pub 5/21/2006. PMID: 16728977 PMCID: PMC3190580

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

Shi X, Kornberg A (2005) Endopolyphosphatase in Saccharomyces cerevisiae undergoes post-translational activations to produce short-chain polyphosphates. FEBS Lett 579(9):2014-8, 3/28/2005. PMID: 15792812

Shi X, Rao NN, Kornberg A. (2004) 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. PMID: 15572452 PMCID: PMC535361

Related Department

Biochemistry and Molecular Biology


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