Personal Introduction

Dr. Bing Li received his BS degree from Beijing Agricultural University, Master degree from Peking University and PHD degree from the Penn State University. After his postdoctoral training with Dr. Jerry Workman at Stowers Institute for Medical Research, Dr. Li joined the faculty of UT Southwestern Medical Center as WA "Tex" Moncrief, Jr. Scholar in Medical Research in 2008. In 2017, Dr. Li became a Professor and Chair of the Department of Biochemistry and Molecular Cell Biology at Shanghai Jiao Tong University School of Medicine. Dr. Li has made a series of discoveries on epigenetic pathways that safeguard chromosome integrity of transcribed regions and has developed cutting-edge biochemical, genomic and proteomic technologies to tackle long-standing conceptual and technical challenges. He authored and co-authored 50+ papers, including Science, Cell and Nature, which have been cited for more than 11,000 times. He also received numerous awards such as Basil O’Connor Scholar Research Award from March of Dimes Foundation in 2011.

Our group has long been committed to the basic research of chromatin biology and gene expression regulation. In recent years, we have focused on both the basic and translational research of cancer epigenetics, as well as the exploration of the molecular mechanism of early embryonic development regulation. Specific research directions include: (1) Structural and functional studies of epigenetic regulators and development of next-generation anti-cancer drugs: We will explore the high-order assembly of transcription machinery and their spatial-temporal regulation in the three dimensional chromosomal environment; we will leverage our mechanistic understanding of regulatory specificity of multi-subunit epigenetic complexes to develop new drug targets and therapeutic strategies; (2) We will explore the molecular mechanisms of epigenetic reprogramming in physiological processes including acquired trait inheritance, stem cell lineage differentiation, T cell activation and sperm development etc., and develop clinical applications to relevant diseases.

Research Grants

• The National Natural Science Foundation of China, 31872817, 2019.01-2022.12, ￥600,000, PI

• The National Key Research and Development Program of China, 2018YFC1004504, 2018.12-2021.12, ￥1,220,000, Sub-project leader

• The Key project of National Natural Science Foundation of China, 32030019, 2021.01-2025.12, ￥2,840,000, PI

• The National Key Research and Development Program of China, 2021YFA1300102, 2021.12-2026.11, ￥4,160,000, Sub-project leader

Publications

1. Caiqing Hao, Xianyu Shao, Juan Song , Mengyuan Peng, Yimin Lao, Ryan Mack, Lei Zhang, Wei Wei, Na Liu, Tian Wang, Yuanyuan Wu, Lanyao Feng, Lijun Yin, Shouxin Wang, Xiaojian Sun, Saijuan Chen, Jiwang Zhang*, Bing Li*（2022）SIRT2 regulates proliferation and chemotherapy response of MLL-ENL-driven acute myeloid leukemia。 Biochem. Biophys. Res. Commun.596:36-42. doi: 10.1016/j.bbrc.2022.01.081.

2. Jingdong Xue, Wanli Yang, Mengyuan Peng and Bing Li (2021) The TFIID Pivot of Preinitiation Complex SCIENCE CHINA Life Sciences (12):2214-2217 doi: 10.1007/s11427-021-2015-6

3. Wen Shao, Xianju Bi, Yixuan Pan, Boyang Gao1, Jun Wu, Yafei Yin, Zhimin Liu, Mengyuan Peng, Wenhao Zhang, Xu Jiang, Wenlin Ren, Yanhui Xu, Zhongyang Wu, Kaili Wang, Ge Zhan,J. Yuyang Lu, Xue Han, Tong Li, Jianlong Wang, Guohong Li, Haiteng Deng, Bing Li*, Xiaohua Shen* (2021) Phase separation of RNA-binding protein promotes polymerase binding and transcription Nature Chemical Biology 18(1):70-80. https://doi.org/10.1038/s41589-021-00904-5 (*co-correspondence)

4. Tao Wang, Juan Song, Min Qu, Xu Gao, Wenhui Zhang, Ziwei Wang, Lin Zhao, Yan Wang, Bing Li*, Jing Li* and Jinjian Yang* (2021) Integrative Epigenome Map of the Normal Human Prostate Provides Insights Into Prostate Cancer Predisposition Front. Cell Dev. Biol. 9:723676. doi.org/10.3389/fcell.2021.723676 (*co-correspondence)

5. Hongye Wang, Yile Huang, Ming Yu, Yang Yu, Sheng Li, Huating Wang, Hao Sun, Bing Li, Guoliang Xu, Ping Hu (2021) Muscle regeneration controlled by a designated DNA dioxygenase Cell Death & Disease 12(6):535

6. Dian-Jia Liu, Fan Zhang, Yi Chen, Yi Jin, Yuan-Liang Zhang, Shu-Bei Chen, Yin-Yin Xie, Qiu-Hua Huang, Wei-Li Zhao, Lan Wang, Peng-Fei Xu, Zhu Chen, Sai-Juan Chen, Bing Li, Aijun Zhang, Xiao-Jian Sun (2020) setd2 knockout zebrafish is viable and fertile: differential and developmental-stress-related requirements for Setd2 and histone H3K36 trimethylation in different vertebrate animals Cell Discovery 6:72

7. Xu Zhu*, Bingxue Lan*, Xianfu Yi*, Chaoran He, Lin Dang, Xingquan Zhou, Yumei Lu, Yongzhan Sun, Zhiheng Liu, Xue Bai, Kai Zhang, Bing Li, Mulin Jun Li, Yupeng Chen, Lirong Zhang (2020) HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription Nucleic Acids Research 48(12):6563-6582

8. Julia V. DiFiore, Travis S. Ptacek, Yi Wang, Bing Li, Jeremy Simon and Brian D. Strahl (2020) Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions Cell Reports 31(10):107751

9. Yanhua Du, Jun Lin, Rulin Zhang, Wanli Yang, Heng Quan, Lijuan Zang, Yaqin Han, Bing Li, Hong Sun and Jun Wu (2019) Ubiquitin Specific Peptidase 5 Promotes Ovarian Cancer Cell Proliferation Through Deubiquitinating HDAC2 Aging 11(21):9778-9793

10. Wei Wang, Jun Xu, Oliver Limbo, Jia Fei, George A. Kassavetis, Jenny Chong, James T. Kadonaga, Paul Russell, Bing Li* and Dong Wang (2019) Molecular basis of chromatin remodeling by Rhp26, a yeast CSB ortholog Proc Natl Acad Sci USA. 116(13):6120-6129 (*co-correspondence)

11. Jun Wu, Yimin Lao and Bing Li (2019) Nuclear actin switch of the INO80 remodeler J Mol Cell Biol. 2019 May 1;11(5):343-344

12. Buki Kwon, Palinda Ruvan Munashingha, Yong-Keol Shin, Chul-Hwan Lee, Bing Li and Yeon-Soo Seo (2016) Physical and functional interactions between nucleosomes and Rad27, a critical component of DNA processing during DNA metabolism The FEBS Journal 283(23):4247-4262

13. Stephen McDaniel, Jennifer Fligor, Chun Ruan, Haochen Cui, Joseph Bridgers, Julia DiFiorea, Angela Gud, Bing Li, and Brian Strahl (2016) Combinatorial histone readout by the dual PHD domains of Rco1 mediates Rpd3S chromatin recruitment and the maintenance of transcriptional fidelity J. Biol. Chem. 291(28):14796-802

14. Andria Schibler, Evangelia Koutelou, Junya Tomida, Marenda Wilson-Pham, Li Wang, Yue Lu, Alexa Parra Cabrera, Renee J. Chosed, Wenqian Li, Bing Li, Xiaobing Shi, Richard D. Wood, and Sharon Y.R. Dent (2016) Histone H3K4 methylation regulates deactivation of the Spindle Assembly Checkpoint through direct binding of Mad2 Genes& Development 30(10):1187-97

15. Chun Ruan, Haochen Cui, Chul-Hwan Lee, Sheng Li and Bing Li (2016) Homodimeric PHD-domain containing Rco1 constitutes a critical interaction hub within the Rpd3S histone deacetylase complex J. Biol. Chem. 291(10):5428-38

16. Joshua Mayfield, Shuang Fan, Shuo Wei, Mengmeng Zhang, Bing Li, Andrew Ellington, Felicia Etzkorn, and Yan Jessie Zhang (2015) Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II ACS Chem Biol. 2015 Sep 15. [Epub ahead of print]

17. Yi Wang, Yanling Niu and Bing Li (2015) Balancing acts of SRI and an auto-inhibitory domain specify Set2 function at transcribed chromatin Nucleic Acids Research 43(10):4881-92. PMCID: PMC4446442

18. Chun Ruan, Chul-Hwan Lee, Haochen Cui, Sheng Li and Bing Li (2015) Nucleosome contact triggers conformational changes of Rpd3S driving high affinity H3K36me nucleosome engagement Cell Reports 10(2): 204-215

19. Chun Ruan and Bing Li (2014) Reading Histone Modifications Fundamentals of Chromatin, edited by J.L. Workman and S.M. Abmayr

20. Daniel S. Ginsburg, Timi Elvuchio Anlembom, Jianing Wang, Sanket R. Patel, Bing Li, and Alan G. Hinnebusch (2014) NuA4 links methylation of histone H3 lysines 4 and 36 to acetylation of histones H4 and H3 J. Biol. Chem. 289(47):32656-70 PMCID: PMC4239618

21. Hong Wen, Yuanyuan Li, Yuanxin Xi, Shiming Jiang, Sabrina Stratton, Danni Peng, Kaori Tanaka, Yongfeng Ren, Zheng Xia, Jun Wu, Bing Li, Michelle Barton, Wei Li, Haitao Li and Xiaobing Shi (2014) ZMYND11 links histone H3.3 K36 trimethylation to transcription elongation and tumor suppression Nature 508(7495):263-8 PMCID: PMC4142212

22. Chul-Hwan Lee, Jun Wu and Bing Li (2013) Chromatin remodelers fine-tune H3K36me-directed deacetylation of neighbor nucleosomes by Rpd3S. Molecular Cell 52(2):255-63

23. Miyong Yun, Chun Ruan, Jae-Wan Huh and Bing Li (2012) Reconstitution of modified chromatin templates for in vitro functional assays. Methods Mol Biol. 833:237-53.

24. Jae-Wan Huh, Jun Wu, Chul-Hwan Lee, Miyong Yun, Daniel Gilada, Chad A. Brautigam and Bing Li (2012) Multivalent di-nucleosome recognition enables the Rpd3S histone deacetylase complex to tolerate decreased H3K36 methylation levels. EMBO J. 31(17):3564-74

25. Xiao-Fen Chen, Benjamin Kuryan, Tasuku Kitada, Nancy Tran, Jing-Yu Li, Siavash Kurdistani, Michael Grunstein, Bing Li and Michael Carey (2011) The Rpd3 Core Complex Is a Chromatin Stabilization Module Curr Biol. 22(1):56-63

26. Yuwen Ke, Jae-Wan Huh, Ross Warrington, Bing Li, Nan Wu, Mei Leng, Junmei Zhang, Haydn L Ball, Bing Li and Hongtao Yu (2011) PICH and BLM limit histone association with anaphase centromeric DNA threads and promote their resolution. EMBO J 30(16):3309-21

27. Miyong Yun, Jun Wu, Jerry Workman and Bing Li (2011) Readers of histone modifications. Cell Research 21:564–578

28. Ling Cai, Benjamin Sutter, Bing Li and Benjamin P. Tu (2011) Acetyl-CoA Induces Cell Growth and Proliferation by Promoting the Acetylation of Histones at Growth Genes.Molecular Cell 42, 426-437

29. Chhabi Govind, Hongfang Qiu, Daniel Ginsburg, Chun Ruan, Kimberly Hofmeyer, Cuihua Hu, Venkatesh Swaminathan, Jerry Workman, Bing Li and Alan G. Hinnebusch (2010) Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes Molecular Cell 39, 234-246

30. Mihaela Sardiu, Joshua Gilmore, Michael Carrozza, Bing Li, Jerry Workman, Laurence Florens, Michael Washburn (2009) Determining Protein Complex Connectivity Using a Probabilistic Deletion Network Derived from Quantitative Proteomics. PLoS One 4(10):e7310

31. Raymond Camahort, Manjunatha Shivaraju, Mark Mattingly, Bing Li, Shima Nakanishi, Dongxiao Zhu, Ali Shilatifard, Jerry L. Workman and Jennifer L. Gerton (2009) Cse4 is Part of an Octameric Nucleosome in Budding Yeast. Molecular Cell 35(6):794-805

32. Bing Li, Jessica Jackson, Matthew D. Simon, Brian Fleharty, Madelaine Gogol, Chris Seidel, Jerry L. Workman and Ali Shilatifard (2009) Histone H3 lysine 36 di-methylation (H3K36me2) is sufficient to recruit the Rpd3S histone deacetylase complex and to repress spurious transcription. J. Biol. Chem. 284(12):7970-6

33. Chia-Hui Lin, Bing Li, Selene Swanson, Ying Zhang, Laurence Florens, Michael P. Washburn, Susan M. Abmayr and Jerry L. Workman (2008) Heterochromatin Protein 1a stimulates histone H3 lysine 36 demethylation by the Drosophila KDM4A demethylase. Molecular Cell 32(5):696-706

34. Tuba Sural, Shouyong Peng, Bing Li, Jerry L. Workman, Peter J. Park, Mitzi I. Kuroda (2008) The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila X chromosome Nature Structural & Molecular Biology (12):1318-25

35. Tamaki Suganuma, Jose L.Gutierrez, Bing Li, Laurence Florens, Selene K. Swanson, Michael P. Washburn, Susan M. Abmayr and Jerry L. Workman (2008) ATAC is a Double Histone Acetyltransferase Complex that Stimulates Nucleosome Sliding Nature Structural & Molecular Biology 15(4):364-72

36. Erica Larschan, Artyom A. Alekseyenko, Andrey A. Gortchakov, Shouyong Peng, Bing Li, Pok Yang, Jerry L. Workman, Peter J. Park, and Mitzi I. Kuroda (2007) MSL Complex Is Attracted to Genes Marked by H3K36 Trimethylation Using a Sequence-Independent Mechanism Molecular Cell 28(1): 121-133

37. Bing Li, Michael Carey and Jerry Workman (2007) The role of chromatin during transcription Cell 128(4):707-19

38. Raymond Camahort, Bing Li, Laurence Florens, Selene Swanson, Michael Washburn, and Jennifer Gerton (2007) Scm3 is essential to recruit the histone H3 variant Cse4 to centromeres and to maintain a functional kinetochore Molecular Cell 26(6):853-65

39. Bing Li, Madelaine Gogol, Mike Carey, Samantha Pattenden, Chris Seidel and Jerry Workman (2007) Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription Genes& Development 21(11):1422-30

40. Bing Li, Madelaine Gogol, Mike Carey, Daeyoup Lee, Chris Seidel and Jerry Workman (2007) Combined action of PHD and Chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science 316, 1050-1054

41. Michael Carey, Bing Li, Jerry L. Workman (2006) RSC Exploits Histone Acetylation to Abrogate the Nucleosomal Block to RNA Polymerase II Elongation Molecular Cell 24, 481-487

42. Wei-Jong Shia, Bing Li, and Jerry L. Workman (2006) SAS-mediated acetylation of histone H4 Lys 16 is required for H2A.Z incorporation at subtelomeric regions in Saccharomyces cerevisiae Genes &Development 20: 2507-2512

43. Jingji Jin, Yong Cai, Bing Li, Ronald C. Conaway, Jerry L. Workman, Joan W.Conaway and Thomas Kusch (2005)   In and out: histone variant exchange in chromatin. Trends in Biochem Sci. 30(12): 680-687

44. Bing Li, Chun Ruan and Jerry Workman (2005) Histones: should I stay or should I go? Genome Biology 6:306

45. Bing Li, Samantha Pattenden, Daeyoup Lee, José Gutiérrez, Jie Chen, Chris Seidel, Jennifer Gerton and Jerry Workman (2005) Preferential occupancy of histone variant H2AZ at inactive promoters influence local histone modifications and chromatin remodeling Proc. Natl. Acad. Sci. USA 102(51): 18385-18390

46. Michael. Carrozza, Bing Li, Laurence Florens, Tamaki Suganuma, Selene Swanson, Kenneth Lee,Wei-Jong Shia, Scott Anderson, John Yates, Michael Washburn and Jerry Workman (2005)   Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription Cell 123(4):581-92

47. Daeyoup Lee, Elena Ezhkova, Bing Li, Samantha Pattenden, William Tansey, Jerry Workman (2005) The Proteasome Regulatory Particle Alters the SAGA Coactivator to Enhance Its Interactions with Transcriptional Activators. Cell 123(3):423-36.

48. Yong Cai, Jing Jin, Laurence Florens, Selene Swanson, Thomas Kusch, Bing Li, Jerry Workman, Michael Washburn, Ronald Conaway, and Joan Conaway (2005) The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. J Biol. Chem 280(14):13665-70

49. Philippe Prochasson, Kristen E. Neely, Ahmed H. Hassan, Bing Li and Jerry L. Workman (2003) Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator interaction domains Molecular Cell 12(4):983-990

50. Bing Li, LeAnn Howe, Scott Anderson, John Yates III and Jerry Workman (2003) The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II J Biol. Chem. 278(11):8897-8903

51. Vishva M. Sharma, Bing Li, and Joseph Reese (2003) SWI/SNF dependent chromatin remodeling of RNR3 requires TAFIIs and the general transcription machinery Genes Dev. 17: 502-515

52. Bing Li and Joseph Reese (2001) Ssn6-Tup1 Regulates RNR3 by Positioning Nucleosomes and Affecting the Chromatin Structure at the Upstream Repression Sequence. J. Biol. Chem. 276(36): 33788-97.

53. Bing Li and Joseph Reese (2000) Derepression of DNA Damage-Regulated Genes Requires Yeast TBP-Associated Factors EMBO J. 19(15):4091-100

54. Bing Li, Cheng Gu and Jindong Zhao (1998) Molecular cloning and expression of pfu DNA polymerase, and its application in long-distance PCR Chinese Science Bulletin 43(10):863-867