Dr. Yang’s research expertise is on structural bases of epigenetic regulation of biological processes, including histone modifications and DNA methylation, as well as nucleic acid-protein interactions. Current focus of Dr. Yang’s group is on the study of molecular mechanisms of epigenetic regulation in infection and immunity. By studying the interaction and interference between pathogenic proteins and host epigenetic factors, they aim to reveal pathogenic mechanisms of various microbes. Drug target validation and structure-based drug design will be carried out to facilitate the development of effective therapeutics for prevention and treatment of pathogenic infections. 

The lab principally uses structure-based approaches to reveal the relationship between macromolecular structures and their functions. Virtual screening (CADD and AIDD) and rational drug design based on the solved structures will also be used. Finally, candidate compounds will be evaluated and optimized by iterative Structure-Activity Relationship (SAR) analyses. 

Their specific research directions include: 

1.Epigenetic mechanisms governing gene expression involved in microbe-host interactions. 2.Mechanisms by which pathogenic proteins influence higher-order structures of host chromatin. 3.Roles of epigenetic factors during T cell development, and chemical intervention of T cell exhaustion by targeting epigenetic factors.

B.S 2000, Biophysics, School of Life Sciences, Peking University 

Ph.D 2005, Biochemistry & Molecular biology, Institute of Biophysics, Chinese Academy of Sciences (CAS)

2006.04-2008.09, Postdoc, Shenzhen Graduate School, Peking University 

2008.10-2013.11, Associate Investigator, Institute of Biophysics, CAS 

2013.12-2017.04, Investigator, Institute of Biophysics, CAS 

2015.10-2017.04, Professor, College of Life Sciences, University of the Chinese Academy of Sciences 

2017.04-2024.11, Professor, College of Pharmacy, Nankai University 

2024.11-present, Principle Investigator, Institute of Microbiology, CAS 

Professional Services 

2021-present, Vice president, Molecular Biophysics Section of the Chinese Biophysical Society 

2015-2021, Secretary General, Molecular Biophysics Section of the Chinese Biophysical Society 

2019-present, Board member, Epigenetics Section of the Genetics Society of China 

2016-2021, Board member, Chinese Crystallographic society 

2015-2019, Member, Youth Federation of the Chinese Academy of Sciences 

2014-2023, Consultant, Commission on Biological Macromolecules, International Union of Crystallography (IUCr) 

2018-2019, Young scientist of World Economic Forum

2019 15th Science and Technology Award for Youth, Tianjin 

2019 Bring in leading Innovative Talent of Tianjin City 

2018 Science and Technology Award of Beijing Municipality, Second prize 

2017 Distinguished Young Scholars of Tianjin City 

2016 National Excellent Young Scientists 

2015 Excellent Member of the Youth Innovation Promotion Association of CAS 

2011 Lu Jiaxi Young Talent Award of Chinese Academy of Sciences 

2011 Member of the Youth Innovation Promotion Association of CAS 

2006 First prize of Chinese Post Doctor Award 

2005 President prize of Chinese Academy of Sciences 

2004 First prize of Director Scholarship of Institute of Biophysics, CAS 

2001 Scholarship of Excellent Graduate Student in the graduate school of CAS

Mechanism of the allosteric activation of epigenetic modification enzyme and rational drug design

1. Shi, F.D.#, Zhang, K.#, Cheng, Q.X., Che, S.Y., Zhi, S.X., Yu, Z.Y., Liu, F., Duan, F.F., Wang, Y.M.* and Yang, N.* (2024) Molecular mechanism governing RNA-binding property of mammalian TRIM71 protein. Science Bulletin, Vol. 69, 72–81.
2. Yang, J.#, Dan, J.M.#, Zhao, N.N., Liu, L.L., Wang, H.S., Liu, Q.Q., Wang, L.L., Li, J., Wu, Y.W., Chen, F.L., Fu, W.L., Liu, F., Lin, M.Q., Zhang, W.Y., Chen, F.Q., Liu, X.Q., Lv, X.Y., Chen, Q., Wu, X.D., Niu, Y.Y.*, Yang, N.*, Zhu, Y.S.*, Long, J.F.*, Liu, L.* (2024) Zscan4 mediates ubiquitination and degradation of co-repressor complex to promote chromatin accessibility in 2C-like cells. Proc. Natl. Acad. Sci. USA, in press.
3. Liu, F., Wang, J.*, Xu, R.M.* and Yang, N.* (2023) Energy landscape quantifications of histone H3.3 recognition by chaperon DAXX reveal an uncoupled binding specificity and affinity. Physical Chemistry Chemical Physics, Vol. 25, 27981–27993.
4. Liu, C.P.#, Yu, Z.#, Xiong, J.#, Hu, J.#, Song, A.#, Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B.*, Li, G.* and Xu, R.M.* (2023) Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1. Science, Vol. 381, eadd8673.
5. Liu, F.#, Pang, N.N.#, Xu, R.M. and Yang, N.* (2023) Mechanism and design of allosteric activators of SIRT1. Protein & Cell, Vol. 14, 387-392.
6. Sun, J.X., Liu, F., Yuan, L.X., Pang, N.N., Zhu, B. and Yang, N.* (2023) Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination, revealed by multi-scale molecular dynamics simulations. Science China Life Sciences, Vol. 66, 313-323.
7. Pang, N.N.#, Sun, J.X.#, Che, S.Y. and Yang, N.* (2022) Structural study of fungus-specific histone deacetylase Hos3 and insight into developing selective inhibitors with antifungal activity. Journal of Biological Chemistry, Vol. 298, 102068.
8. Ma, S.#, Zhang, J.Y.#, Guo, Q.S., Cao, C., Bao, K.W., Liu, L., Chen, D.G., Liu, Z., Yang, J., Yang, N.*, Yao, Z.* and Shi, L.* (2022) Disrupting PHF8-TOPBP1 connection elicits a breast tumor-specific vulnerability to chemotherapeutics. Cancer Letters, Vol. 530, 29-44.
9. Ma, S.#, Cao, C.#, Che, S.Y.#, Wang, Y.J.#, Su, D.X.#, et al., Yao, Z.*, Yang, N.* and Shi, L.* (2021) PHF8-promoted TOPBP1 demethylation drives ATR activation and preserves genome stability. Science Advances, Vol. 7, eabf7684.
10. Xu, X.#, Wang, M.Z.#, Sun, J.X.#, Yu, Z.Y.#, Li, G.H., Yang, N.* and Xu, R.M.* (2021) Structure specific DNA recognition by the SLX1-SLX4 endonuclease complex. Nucleic Acid Research, Vol. 49, 7740-7752.
11. Sun, J.X.#, Li, Z.B#. and Yang, N.* (2021) Mechanism of the conformational change of the protein methyltransferase SMYD3: a molecular dynamics simulation study. International Journal of Molecular Sciences, Vol. 22, 7185 (1-21).
12. Liu, F. and Yang, N.* (2020) Multiscale landscape of molecular mechanism of SIRT1 activation by STACs. Physical Chemistry Chemical Physics, Vol. 22, 826-837.
13. Song, X.S.#, Yang, L.L.#, Wang, M.Z., Gu, Y., Ye, B.Q., Fan, Z.S., Xu, R.M.* and Yang, N.* (2019) A higher-order configuration of the heterodimeric DOT1L-AF10 coiled-coil domains potentiates their leukemogenenic activity. Proc. Natl. Acad. Sci. USA, Vol. 116, 19917-19923.
14. Sun, J.X., Shi, F.D. and Yang, N.* (2019) Exploration of the substrate preference of lysine methyltransferase SMYD3 by molecular dynamics simulations. ACS Omega, Vol. 4, 19573-19581.
15. Li, Y.#, Duan, F.F.#, Zhao, Y.T., Gu, K.L., Liao, L.Q., Su, H.B., Hao, J., Zhang, K., Yang, N. and Wang Y.M.* (2019) A TRIM71 binding long noncoding RNA Trincr1 represses FGF/ERK signaling in embryonic stem cells. Nature Communications, Vol. 10, 1368.
16. Zhang, L.#, Serra-Cardona, A.#, Zhou, H., Wang, N., Yang, N., Zhang, Z.* and Xu, R.M.* (2018) Multisite substrate recognition in Asf1-dependent acetylation of histone H3 K56 by Rtt109. Cell, Vol. 174, 818-830.
17. Fu, W.Q.#, Liu, N.#, Qiao, Q.#, Wang, M., Min, J.R., Zhu, B.*, Xu, R.M.* and Yang, N.* (2016) Structural Basis for Substrate Preference of SMYD3, A SET Domain-containing Protein Lysine Methyltransferase. Journal of Biological Chemistry, Vol. 291, 9173-9180.
18. Fang, D.#, Gan, H.#, Lee, J.H.#, Han, J.#, Wang, Z.#, Riester, S.M., Jin, L., Chen, J., Zhou, H., Wang, J., Zhang, H., Yang, N., Bradley, E.W., Ho, T.H., Rubin, B.P., Bridge, J.A., Thibodeau, S.N., Ordog, T., Chen, Y., van Wijnen, A.J., Oliveira, A.M., Xu, R.M., Westendorf, J.J. and Zhang, Z.* (2016) The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas. Science, Vol. 29, 1316-1325.
19. Cao, D.F., Wang, M., Qiu, X.Y., Liu, D.X., Jiang, H.L., Yang, N.* and Xu, R.M.* (2015) Structural basis for allosteric, substrate-dependent stimulation of SIRT1 activity by resveratrol. Genes & Development, Vol. 29, 1316-1325.
20. Yang, D.X.#, Fang, Q.L.#, Wang, M.#, Ren, R., Wang, H., He, M., Sun, Y.W., Yang, N.* and Xu, R.M.* (2013) Nα-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain. Nature Structural & Molecular Biology, Vol. 20, 1116-1118.