Xiao-Bing Shi Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, USA
1 protocol

Hong Wen Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, USA
1 protocol

Yuan-Yuan Li MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, China
1 protocol

Hai-Tao Li
  • MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, China
Research focus
  • Biochemistry
  • 1 Author merit


Ph.D. in Molecular Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 2003

Current position

Professor in Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China

Publications (since 2002)

  1. Zhao, S. and Li, H.* (2015). Crystallography-based mechanistic insights into epigenetic regulation. In: Zheng, Y. G. (ed). Epigenetic technological applications. Elsevier Publisher. (Book chapter)
  2. Li, H.*, Zhao, S. and Patel, D. J. (2015). Histone recognition by tandem modules and modulation by multiple PTMs. In: Zhou, M. M. (ed). Life sciences and biomedicine: histone recognition. Springer. (Book chapter)
  3. Noh, K. M., Maze, I., Zhao, D., Xiang, B., Wenderski, W., Lewis, P. W., Shen, L., Li, H.* and Allis, C. D.* (2014). ATRX tolerates activity-dependent histone H3 methyl/phos switching to maintain repetitive element silencing in neurons. Proc Natl Acad Sci U S A.
  4. Li, Y., Wen, H., Xi, Y., Tanaka, K., Wang, H., Peng, D., Ren, Y., Jin, Q., Dent, S. Y., Li, W., Li, H.* and Shi, X.* (2014). AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylation. Cell 159(3): 558-571.
  5. Li, J., Li, Y., He, Q., Li, Y., Li, H. and Liu, L. (2014). One-pot native chemical ligation of peptide hydrazides enables total synthesis of modified histones. Org Biomol Chem 12(29): 5435-5441.
  6. Wen, H., Li, Y., Li, H. and Shi, X. (2014). ZMYND11: an H3.3-specific reader of H3K36me3. Cell Cycle 13(14): 2153-2154.
  7. Wen, H., Li, Y., Xi, Y., Jiang, S., Stratton, S., Peng, D., Tanaka, K., Ren, Y., Xia, Z., Wu, J., Li, B., Barton, M. C., Li, W.*, Li, H.* and Shi, X.* (2014). ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 508(7495): 263-268.
  8. Su, X., Zhu, G., Ding, X., Lee, S. Y., Dou, Y., Zhu, B., Wu, W.* and Li, H.* (2014). Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Genes Dev 28(6): 622-636.
  9. Wee, S., Dhanak, D., Li, H., Armstrong, S. A., Copeland, R. A., Sims, R., Baylin, S. B., Liu, X. S. and Schweizer, L. (2014). Targeting epigenetic regulators for cancer therapy. Ann N Y Acad Sci 1309: 30-36.
  10. Zheng, X., Gooi, L. M., Wason, A., Gabriel, E., Mehrjardi, N. Z., Yang, Q., Zhang, X., Debec, A., Basiri, M. L. and Avidor-Reiss, T. (2014). Conserved TCP domain of Sas-4/CPAP is essential for pericentriolar material tethering during centrosome biogenesis. Proc Natl Acad Sci USA 111(3): E354-E363.
  11. Qian, M. X., Pang, Y., Liu, C. H., Haratake, K., Du, B. Y., Ji, D. Y., Wang, G. F., Zhu, Q. Q., Song, W., Yu, Y., Zhang, X. X., Huang, H. T., Miao, S., Chen, L. B., Zhang, Z. H., Liang, Y. N., Liu, S., Cha, H., Yang, D., Zhai, Y., Komatsu, T., Tsuruta, F., Li, H., Cao, C., Li, W., Li, G. H., Cheng, Y., Chiba, T., Wang, L., Goldberg, A. L., Shen, Y. and Qiu, X. B. (2013). Acetylation-mediated proteasomal degradation of core histones during DNA repair and spermatogenesis. Cell 153(5): 1012-1024.
  12. Ratnakumar, K., Duarte, L. F., LeRoy, G., Hasson, D., Smeets, D., Vardabasso, C., Bonisch, C., Zeng, T., Xiang, B., Zhang, D. Y., Li, H., Wang, X., Hake, S. B., Schermelleh, L., Garcia, B. A. and Bernstein, E. (2012). ATRX-mediated chromatin association of histone variant macroH2A1 regulates alpha-globin expression. Genes Dev 26(5): 433-438.
  13. Li, Y. and Li, H.* (2012). Many keys to push: diversifying the 'readership' of plant homeodomain fingers. Acta Biochim Biophys Sin (Shanghai) 44(1): 28-39.
  14. Iwase, S., Xiang, B., Ghosh, S., Ren, T., Lewis, P. W., Cochrane, J. C., Allis, C. D., Picketts, D. J., Patel, D. J.*, Li, H.* and Shi, Y.* (2011). ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Nat Struct Mol Biol 18(7): 769-776.
  15. Rajakumara, E., Wang, Z., Ma, H., Hu, L., Chen, H., Lin, Y., Guo, R., Wu, F., Li, H., Lan, F., Shi, Y. G., Xu, Y., Patel, D. J. and Shi, Y. (2011). PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol Cell 43(2): 275-284.
  16. Ruthenburg, A. J., Li, H., Milne, T. A., Dewell, S., McGinty, R. K., Yuen, M., Ueberheide, B., Dou, Y., Muir, T. W., Patel, D. J. and Allis, C. D. (2011). Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 145(5): 692-706.
  17. Wang, Y., Ludwig, J., Schuberth, C., Goldeck, M., Schlee, M., Li, H., Juranek, S., Sheng, G., Micura, R., Tuschl, T., Hartmann, G. and Patel, D. J. (2010). Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I. Nat Struct Mol Biol 17(7): 781-787.
  18. Wang, Z., Song, J., Milne, T. A., Wang, G. G., Li, H., Allis, C. D. and Patel, D. J. (2010). Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression. Cell 141(7): 1183-1194.
  19. Lu, J., Li, H., Zhang, J., Li, M., Liu, M. Y., An, X., Liu, M. C. and Chang, W. (2010). Crystal structures of SULT1A2 and SULT1A1 *3: insights into the substrate inhibition and the role of Tyr149 in SULT1A2. Biochem Biophys Res Commun 396(2): 429-434.
  20. Wang, Y., Juranek, S., Li, H., Sheng, G., Wardle, G. S., Tuschl, T. and Patel, D. J. (2009). Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461(7265): 754-761.
  21. Wang, G. G., Song, J., Wang, Z., Dormann, H. L., Casadio, F., Li, H., Luo, J. L., Patel, D. J. and Allis, C. D. (2009). Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger. Nature 459(7248): 847-851.
  22. Li, H.#, Motamedi, M. R.#, Yip, C. K., Wang, Z., Walz, T., Patel, D. J. and Moazed, D. (2009). An alpha motif at Tas3 C terminus mediates RITS cis spreading and promotes heterochromatic gene silencing. Mol Cell 34(2): 155-167. (#Equal contribution)
  23. Zhao, Q., Rank, G., Tan, Y. T., Li, H., Moritz, R. L., Simpson, R. J., Cerruti, L., Curtis, D. J., Patel, D. J., Allis, C. D., Cunningham, J. M. and Jane, S. M. (2009). PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat Struct Mol Biol 16(3): 304-311.
  24. Xiao, A., Li, H., Shechter, D., Ahn, S. H., Fabrizio, L. A., Erdjument-Bromage, H., Ishibe-Murakami, S., Wang, B., Tempst, P., Hofmann, K., Patel, D. J., Elledge, S. J. and Allis, C. D. (2009). WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature 457(7225): 57-62.
  25. Wang, Y., Juranek, S., Li, H., Sheng, G., Tuschl, T. and Patel, D. J. (2008). Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456(7224): 921-926.
  26. Ruthenburg, A. J., Li, H., Patel, D. J. and Allis, C. D. (2007). Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol 8(12): 983-994.
  27. Taverna, S. D.#*, Li, H. *, Ruthenburg, A. J., Allis, C. D. and Patel, D. J. (2007). How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14(11): 1025-1040. (#Equal contribution)
  28. Li, H., Fischle, W., Wang, W., Duncan, E. M., Liang, L., Murakami-Ishibe, S., Allis, C. D. and Patel, D. J. (2007). Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger. Mol Cell 28(4): 677-691.
  29. Taverna, S. D., Ilin, S., Rogers, R. S., Tanny, J. C., Lavender, H., Li, H., Baker, L., Boyle, J., Blair, L. P., Chait, B. T., Patel, D. J., Aitchison, J. D., Tackett, A. J. and Allis, C. D. (2006). Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell 24(5): 785-796.
  30. Ruthenburg, A. J., Wang, W., Graybosch, D. M., Li, H., Allis, C. D., Patel, D. J. and Verdine, G. L. (2006). Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat Struct Mol Biol 13(8): 704-712.
  31. Li, H., Ilin, S., Wang, W., Duncan, E. M., Wysocka, J., Allis, C. D. and Patel, D. J. (2006). Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442(7098): 91-95.
  32. Li, H. T., Chang, T., Chang, W. C., Chen, C. J., Liu, M. Y., Gui, L. L., Zhang, J. P., An, X. M. and Chang, W. R. (2005). Crystal structure of C-terminal desundecapeptide nitrite reductase from Achromobacter cycloclastes. Biochem Biophys Res Commun 338(4): 1935-1942.
  33. Lu, J. H.#, Li, H. T.#, Liu, M. C., Zhang, J. P., Li, M., An, X. M. and Chang, W. R. (2005). Crystal structure of human sulfotransferase SULT1A3 in complex with dopamine and 3'-phosphoadenosine 5'-phosphate. Biochem Biophys Res Commun 335(2): 417-423. (#Equal contribution)
  34. Li, H. T., Wang, C., Chang, T., Chang, W. C., Liu, M. Y., Le Gall, J., Gui, L. L., Zhang, J. P., An, X. M. and Chang, W. R. (2004). pH-profile crystal structure studies of C-terminal despentapeptide nitrite reductase from Achromobacter cycloclastes. Biochem Biophys Res Commun 316(1): 107-113.
  35. Li, H. T., Chang, T., Liu, M. Y., Le Gall, J., An, X. M., Gui, L. L., Zhang, J. P., Liang, D. C. and Chang, W. R. (2002). Preliminary crystallographic studies of two C-terminally truncated copper-containing nitrite reductases from Achromobacter cycloclastes: changed crystallizing behaviors caused by residue deletion. Biochem Biophys Res Commun 299(2): 173-176.
1 Protocol published
Determination of Protein-DNA (ZMYND11-DNA) Interaction by a Label-Free Biolayer Interferometry Assay
Authors:  Yuan-Yuan Li, Hong Wen, Xiao-Bing Shi and Hai-Tao Li, date: 02/20/2015, view: 9960, Q&A: 0
This protocol describes a robust technique for the measurement of ZMYND11-DNA interaction by a label-free Biolayer Interferometry (BLI). ZMYND11 is a novel histone reader protein that specifically recognizes H3.3K36me3 via its tandem Bromodomain, ...
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