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 - 2012Deputy Director, Institute of Biophysics (IBP), CAS

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

2012 - 2013Director, Bureau of Life Sciences and Biotechnology, CAS

2013 - Director, Bureau of Frontier Sciences and Education, 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

2013 -Vice President, the Chinese Biophysical Society

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) N-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain. Nat. Struct. Mol. Biol.20, 1116-1118.

(50)F. Song, P. Chen, D. Sun, M. Wang, L. Dong, D. Liang, R.M. Xu, P. Zhu, and G. Li (2014) Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science344, 376-380.

(51)R. Ren, H. Liu, W. Wang, M. Wang, N. Yang, Y.H. Dong, W. Gong, R. Lehmann, and R.M. Xu (2014) Structure and domain organization of Drosophila Tudor.Cell Res., doi: 10.1038/cr.2014.63. [Epub ahead of print]

(52)T. Zhou, J. Xiong, M. Wang, N. Yang, J. Wong, B. Zhu, and R.M. Xu (2014)Structural basis for hydroxymethylcytosine recognition by the SRA Domain of UHRF2.Mol. Cell, doi: 10.1016/j.molcel.2014.04.003. [Epub ahead of print]

(53)Y. Li, L. Zhang, T. Liu, C. Chai, Q. Fang, H. Wu, P.A.A. Garcia, Z. Han, S. Zong, Y. Yu, X. Zhang, M.R. Parthun, J. Chai, R.M. Xu, and M. Yang(2014) Hat2p recognizes the histone H3 tail to specify the acetylation of the newly synthesized H3/H4 heterodimer by the Hat1p/Hat2p complex.Genes Dev., doi:10.1101/gad.240531.114. [Published in advance May 16, 2014]