Rui-Ming Xu

Rui-Ming Xu

Curriculum vitae

AddressInstitute of BiophysicsE-mail:

Chinese Academy of SciencesPhone: +86-10-64888797

15 Datun Road, Chaoyang DistrictFax: +86-10-64888513

Beijing 100101, China

Education

Zhejiang University, Hangzhou, ChinaB.Sc.1984Physics

Brandeis University, Waltham, MAM.A.1985Physics

Brandeis University, Waltham, MAPh.D.1990Physics

Positions Held

1984 - 1989Graduate Research, Brandeis University (with L.F. Abbott & M.T. Grisaru)

1989 - 1991Postdoctoral Fellow, University of Texas at Austin (with Steven Weinberg)

1991 - 1993Postdoctoral Associate, SUNY at Stony Brook (with Chen Ning Yang)

1993 - 1994Visiting Scientist, Cold Spring Harbor Laboratory (with Xiaodong Cheng)

1994 - 1996Staff Associate II, Cold Spring Harbor Laboratory (with Xiaodong Cheng)

1996 - 2000Assistant Professor, Cold Spring Harbor Laboratory

1998 - 2006Faculty member, Genetics and Biophysics programs at Stony Brook University

2000 - 2004Associate Professor, Cold Spring Harbor Laboratory

2005 - 2006Professor, Cold Spring Harbor Laboratory

2006 - 2008Professor, Skirball Institute of Biomolecular Medicine & Department of Pharmacology, NYU School of Medicine (Adjunct Professor since 1/1/2009)

2009 - Investigator, Institute of Biophysics, Chinese Academy of Sciences (CAS); and Director designate, National Laboratory of Protein Science, Beijing, China

2010 - Deputy Director, Institute of Biophysics (IBP), CAS

2011 - Director, National Laboratory of Biomacromolecules, IBP, CAS

2012 - Director, Bureau of Life Sciences and Biotechnology, CAS

Awards and Honors

1984China-U.S. Physics Examination and Application (CUSPEA) Fellow

1984Outstanding Thesis Award, Zhejiang University

2008National “Thousand-person Plan” Award

2009Great Wall Professorship, Chinese Academy of Sciences-Novo Nordisk

2009Outstanding Young Investigator Award, Natural Science Foundation of China

2012Fellow, the American Association for the Advancement of Science (AAAS)

Professional Services

1998 - 2004Spokesperson, beamline X26C, National Synchrotron Light Source, BNL

1998Mail-in grant reviewer for the NIH Biochemistry study section

1999, 2003Mail-in grant reviewer for The Wellcome Trust, UK

2001Mail-in reviewer for American Chemical Society Petroleum Research Fund

2001, 2003, 2004Ad hoc reviewer, NIH study section BBCB

2001 - 2004Biology Proposal Study Panel, NSLS, BNL (chair, 2003-2004)

2003Review panel, NIH study section ZRG1 SSS-B

2007Review panel, NIH study section ZAG1 ZIJ-5

2007 Member of assessment panel, China Fellows Program of Cancer Research UK 2008 Review panel, NIH study section ZGM1 BRT-9 (KR)

2007 - Member of Editorial Board, Genes & Development

2008 - Member of Editorial Board, Science in China, Series C: Life Sciences

2008 - Vice President, Cold Spring Harbor Asia

2009 -Member of Executive Committee, Chinese Crystallographic Society

2009 -Member of Executive Committee, and Director of Molecular Biophysics Section, the Chinese Biophysical Society

2010 - Deputy editor-in-chief, Protein & Cell

2010, 2012Co-organizer, Cold Spring Harbor Asia Meeting on “Epigenetics, Chromatin & Transcription”

2011 -Vice President, The Chinese Protein Society

2011 -Member of Editorial Board, BBA-Gene Regulatory Mechanisms

Peer Reviewed Publications (13 earlier ones not listed)

(1)R.M. Xu, G. Carmel, R.M. Sweet, J. Kuret, and X. Cheng (1995) Crystal structure of casein kinase-1, a phosphate-directed protein kinase. EMBO J. 14, 1015-1023.

(2)R.M. Xu, G. Carmel, J. Kuret, and X. Cheng (1996) Structural basis for selectivity of the isoquinoline sulfonamide family of protein kinase inhibitors. Proc. Natl. Acad. Sci. USA, 93, 6308-6313.

(3)R.M. Xu,C. Koch, Y. Liu, J.R. Horton, D. Knapp, K. Nasmyth, and X. Cheng (1997) Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell cycle control of DNA synthesis. Structure5, 349-358.

(4)L. Jokhan, A.P. Dong, A. Mayeda, A.R. Krainer, and R.M. Xu (1997) Crystallization and preliminary X-ray diffraction studies of UP1, the two-RRM domain of hnRNP A1. Acta Cryst.D53, 615-618.

(5)R.M. Xu, L. Jokhan, X. Cheng, A. Mayeda, and A.R. Krainer (1997) Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs. Structure5, 559-570.

(6)A. Mayeda, S.H. Munroe, R.M. Xu, and A.R. Krainer (1998) Distinct functions of the closely related tandem RNA recognition motifs of hnRNP A1. RNA4, 1111-1123.

(7)J. Jiang, Y. Zhang, A.R. Krainer, and R.M. Xu (1999) Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein. Proc. Natl. Acad. Sci. USA 96, 3572-3577.

(8)J. Ding, M.K. Hayashi, A.R. Krainer, and R.M. Xu (1999) Crystal structure of the two-RRM domain hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes & Dev. 13, 1102-1115.

(9)J.P.J. Chong, M.K. Hayashi, M.N. Simon, R.M. Xu, and B. Stillman (2000) A double hexamer archaeal minichromosome maintenance protein is an ATP dependent DNA helicase. Proc. Natl. Acad. Sci. USA 97, 1530-1535.

(10)J. Jiang, D.S. Horowitz, and R.M. Xu (2000) Crystal structure of the functional domain of the splicing factor Prp18. Proc. Natl. Acad. Sci. USA 97, 3022-3027.

(11)J. Min, J. Landry, R. Sternglanz, and R.M. Xu (2001) Crystal structure of a SIR2 homolog-NAD complex. Cell105, 269-279.

(12)J. Vitali, J. Ding, J. Jiang, Y. Zhang, A.R. Krainer, and R.M. Xu (2002) Correlated Alternative Side-chain Conformations in the RNA-Recognition Motif of hnRNP A1. Nucleic Acids Res. 30, 1531-1538.

(13)Z. Zhang, M.K. Hayashi, O. Merkel, B. Stillman, and R.M. Xu (2002) Structure and function of the BAH domain of ORC1 in transcriptional silencing. EMBO J. 21, 4600-4611.

(14)H.H Ng, R.M. Xu, Y. Zhang, and K. Struhl (2002) Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3-Lysine 79. J. Biol. Chem. 277, 34655-34657.

(15)J. Min, X. Zhang, X. Cheng, S.I. Grewal, and R.M. Xu (2002) Structure of the SET domain histone lysine methyltransferase Clr4. Nat. Struct. Biol. 9, 828-832.

(16)J. Min, Q. Feng, Z. Li, Y, Zhang, and R.M. Xu (2003) Structure of the catalytic domain of human Dot1L, a non-SET domain nucleosomal histone methyltransferase. Cell112, 711-723.

(17)H. Shi and R.M. Xu (2003) Crystal structure of the Drosophila Mago nashi -Y14 complex. Genes & Dev. 17, 971-976.

(18)J. Min, Y. Zhang, and R.M. Xu (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at lysine 27. Genes & Dev. 17, 1823-1828.

(19)J. Landry, A. Sutton, T. Hesman, J. Min, R.M. Xu, M. Johnston, and R. Sternglanz (2003) Set2-catalyzed methylation of histone H3 represses basal expression of GAL4 in S. cerevisiae. Mol. Cell Biol. 23, 5972-5978.

(20)H. Chiodi, M. Corioni, M. Giordano, R. Valgardsdottir, F. Cobianchi, R.M. Xu, S. Riva, and G. Biamonti (2004) RNA binding domain 2 directs the recruitment of SF2/ASF to nuclear stress bodies. Nucleic Acids Res.32, 4127-4136.

(21)H. Shi, O. Cordin, C.M. Minder, P. Linder, and R.M. Xu (2004) Crystal structure of the human ATP-dependent splicing and export factor UAP56. Proc. Natl. Acad. Sci. USA101, 17628-17633.

(22)H.C. Hsu, B. Stillman, and R.M. Xu (2005) Structural basis for origin recognition complex 1 protein-silencing regulator 1 protein interaction in epigenetic silencing. Proc. Natl. Acad. Sci. USA102, 8519-8524.

(23)G. Hu, G. Lin, M. Wang, J. Jiang, R.M. Xu, C. Nathan, and H. Li (2006) Structure of the Mycobacterium tuberculosis proteasome and mechanism of inhibition by a peptidyl boronate. Mol. Microbiology59, 1417-1428.

(24)Y. Huang, M.P. Myers, and R.M. Xu (2006) Structure of the EMSY-HP1 complex reveals a new mode of HP1 binding. Structure14, 703-712.

(25)J.J. Connelly, P. Yuan, H.C. Hsu, Z. Li, R.M. Xu*, and R. Sternglanz* (2006) Structure and function of the yeast Sir3 BAH domain. Mol. Cell Biol. 26, 3256-3265. *Co-corresponding authors.

(26)Q.-S. Zhang, L. Manche, R.M. Xu, and A. R. Krainer (2006) HnRNP A1 associates with telomere ends and stimulates telomerase activity by facilitating the translocation step. RNA12, 1116-1128.

(27)Y. Huang, J. Fang, M.T. Bedford, Y, Zhang, and R.M. Xu (2006) Recognition of histone H3 Lysine-4 methylation by the double tudor domain of JMJD2A. Science 312, 748-751.

(28)Z. Li, R. Cao, M. Wang, M.P. Myers, Y. Zhang, and R.M. Xu (2006) Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex. J. Biol. Chem.281, 20643-20649.

(29)J. Han, H. Zhou, B. Horazdovsky, K. Zhang, R.M. Xu, and Z. Zhang (2007) Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science315, 653-655.

(30)J. Han, H. Zhou, Z. Li, R.M. Xu, and Z. Zhang (2007) The Rtt109-Vps75 histone acetyltransferase complex acetylates non-nucleosomal histone H3. J. Biol. Chem.282, 14158-14164.

(31)X. Yang, J. Zhou, L. Sun, Z. Wei, J. Gao, W. Gong, R.M. Xu, Z. Rao, and Y. Liu (2007) Structural basis for DCN-1’s function in protein neddylation. J. Biol. Chem.282, 24490-24494.

(32)J. Han, H. Zhou, Z. Li, R.M. Xu, and Z. Zhang (2007) Acetylation of lysine 56 of histone H3 catalyzed by Rtt109 and regulated by Asf1 is required for replisome integrity. J. Biol. Chem.282, 28587-28596.

(33)H.P. Harding, J.G. Lackey, H.C. Hsu, Y. Zhang, J. Deng, R.M. Xu, M.J. Dhama, and D. Ron (2008) An intact unfolded protein response in Trpt1 knockout mice reveals phylogenetic divergence in pathways for RNA ligation. RNA14, 225-232.

(34)M.K. Hayashi, C. Tang, C. Verpelli, R. Narayanan, M.H. Sterns, R.M. Xu, H. Li, C. Sala, and Y. Hayashi (2009) Structural framework of the postsynaptic density formed by a high-order complex between Homer and Shank. Cell137, 159-171.

(35)Y. Li, P. Trojer, C.F. Xu, P. Cheung, A. Kuo, W.J. 3rd, Drury, Q. Qiao, T.A. Neubert, R.M. Xu, O. Gozani, and D. Reinberg (2009) The target of the NSD family of histone lysine methyl transferases depends on the nature of the substrate.J. Biol. Chem.284, 34283-95.

(36)H. Liu, J.Y. Wang, Y. Huang, Z. Li, W. Gong, R. Lehmann, and R.M. Xu (2010) Structural basis for methylarginine-dependent recognition of Aubergine by Tudor. Genes & Dev24, 1876-81.

(37)Q. Qiao, Y. Li, Z. Chen, M. Wang, D. Reinberg, and R.M. Xu (2011) The structure of NSD1 reveals an autoregulatory mechanism underlying histone H3K36 methylation. J. Biol. Chem.286, 8361-8.

(38)D. Su, Q. Hu, H. Zhou, J.R. Thompson, R.M. Xu, Z. Zhang, and G. Mer (2011) Structure and histone binding properties of the Vps75-Rtt109 chaperone-lysine acetyltransferase complex. J. Biol. Chem.286, 15625-9.

(39)H. Hu, Y. Liu, M. Wang, J. Fang, H. Huang, N. Yang, Y. Li, J. Wang, X. Yao, Y. Shi, G. Li, and R.M. Xu (2011) Structure of a CENP-A-Histone H4 heterodimer in complex with chaperone HJURP. Genes & Dev. 25, 901-6.

(40)W. Wang, Z. Chen, Z. Mao, H. Zhang, X. Ding, S. Chen, X. Zhang, R.M. Xu, B. Zhu (2011) Nucleolar protein Spindlin1 recognizes H3K4 methylation and stimulates the expression of rRNA genes. EMBO Rep.12, 1160-1166.

(41)L. Sun, M. Wang, Z. Lv, N. Yang, Y. Liu, S. Bao, W. Gong, and R.M. Xu (2011) Structural insights into protein arginine symmetric dimethylation by PRMT5. Proc. Natl. Acad. Sci. USA108, 20538-20543.

(42)K. Liu, C. Bian, H. Liu, Y. Guo, R. Lam, F. MacKenzie, L.A. Rojas, D. Reinberg, M. Bedford, R.M. Xu*, and J. Min*(2012) Crystal structureof TDRD3 and methyl-arginine binding characterizations of TDRD3, SMN and SPF30. PLoS ONE7, e30375. *Co-corresponding authors.

(43)P.C. Lin, and R.M. Xu (2012) Structure and assembly of the SF3a splicing factor complex of U2 snRNP. EMBO J.31, 1579-1590.

(44)L. Wang, F. Wang, D. Zhang, Z. Chen, R.M. Xu, K.H. Nierhaus, W. Gong, and Y. Qin (2012) A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases. Nat. Struct. Mol. Biol. 19, 403-410.

(45)N. Yang, W. Wang, Y. Wang, M. Wang, Q. Zhao, Z. Rao, B. Zhu, and R.M. Xu (2012) Distinct mode of methylated lysine-4 of histone H3 recognition by tandem tudor-like domains of Spindlin1. Proc. Natl. Acad. Sci. USA109, 17954-17959.

(46)N. Yang and R.M. Xu (2012) Structure and function of the BAH domain in chromatin biology. Crit. Rev. Biochem. Mol. Biol., Nov. 27, 2012 [Epub ahead of print].

(47)C.P. Liu, C. Xiong, M. Wang, Z. Yu, N. Yang, P. Chen, Z. Zhang, G. Li, and R.M. Xu (2012) Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX, Nat. Struct. Mol. Biol. 19, 1287-1292.

(48)H.C. Hsu, C.L. Wang, M. Wang, N. Yang, Z. Chen, R. Sternglanz, and R.M. Xu (2013) Structural basis for allosteric stimulation of Sir2 activity by Sir4 binding. Genes & Dev. 27, 64-73.

(49)D. Yang, Q. Fang, M. Wang, R. Ren, H. Wang, M. He, Y. Sun, N. Yang, and R.M. Xu (2013) Acetylation of the amino terminus of Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain. Manuscript submitted.

(50)G.M. Kong, Z. Gu., Z. Chen, R.M. Xu, and Z. Wang (2013) Novel small-molecule inhibitors specific for protein arginine methyltransferase 5. Manuscript submitted.