Xiong Ji, Ph.D.
RNA polymerases research group
Associate Professor, College of Life Sciences, Peking University
tel：
E-mail：xiongji@pku.edu.cn
Our lab is focused on understanding the fundamental principles of selective gene expression in mammalian cells. We use early embryonic stem cells and cancer cells as our model system, combine computation theory, genomics, proteomics, bioinformatics, genome editing, imaging and biochemistry techniques. Specific research direction includes:
1）RNA polymerase related molecular mechanisms, diseases and probes
2）Biomolecular computing models and design
This laboratory has long been dedicated to the study of gene expression regulation. Recent research advancements include: 1) Systematic analysis of the functional pision of RNA polymerase II (Pol II) subunits, revealing a non-canonical functional mechanism by which the disassociated RPB3 subunit specifically regulates the 3' end processing of ribosomal protein genes; 2) Development of an efficient method for detecting three-dimensional chromatin structures, demonstrating that RNA polymerases I, II, and III are involved in establishing and maintaining local chromatin higher-order structures, and elucidating a new mechanism by which Pol III coordinates the transcription rate of neighboring Pol II by regulating local chromatin structure; 3) Identification of new factors and mechanisms regulating Pol II-mediated gene expression, including histone β-hydroxybutyrylation modification, the molecular chaperone RUVBL1/2, the histone acetylation recognition factor BRD2, and the transcription factor ZBTB21. Over the past five years, more than 20 high-impact academic papers have been published in internationally renowned journals such as Cell (2023), Molecular Cell (2022, 2023), Nature Communications (2022, 2025), Nucleic Acids Research (2023, 2024), Genome Biology (2020, 2022), Cell Discovery (2020), and Cell Reports (2023).
Zheng HN, Xu QQ, Ji DX, Yang BQ, Ji X. (2025) CTDP1 and RPB7 stabilize Pol II and permit reinitiation. Nat. Commun., 16: 2161.
Liu MT, Xu QQ, Wang H, Ji X. (2025) INO80/SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape. Nucleic Acids Res., 53: gkaf892.
Zhu JY, Bao LJ, Xu SC, Ji X. (2025) FeaSion decodes the regulatory landscape and functional persity of RNA polymerase II CTD phosphorylation. Sci. Adv., 11: eadz2345.
Li Y, Huang J, Bao L, Zhu J, Duan W, Zheng H, Wang H, Jiang Y, Zhang M, Yi CQ, Ji X. (2023) Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits. Mol. Cell, 83: 1280-1297.
Qin F, Li B, Wang H, Ma S, Li J, Liu S, Kong L, Zheng H, Zhu R, Han Y, Yang M, Li K, Ji X, Chen P. (2023) Linking chromatin acylation mark-defined proteome and genome in living cells. Cell, 186: 1066.
Wang H, Li B, Zuo L, Wang B, Yan Y, Tian K, Zhou R, Wang C, Chen X, Jiang Y, Zheng H, Qin F, Zhang B, Yu Y, Liu C, Xu Y, Gao J, Qi Z, Deng W, Ji X. (2022) The transcriptional coactivator RUVBL2 regulates Pol II clustering with perse transcription factors. Nat. Commun., 13: 5703.
Li Y, Huang. J, Zhu J, Bao L, Wang H, Jiang Y, Tian K, Wang R, Zheng H, Duan W, Lai W, Yi X, Zhu Y, Guo T, Ji X. (2022) Targeted protein degradation reveals Pol II heterogeneity and functional persity. Mol. Cell, 82: 3943-3959.
Rui Wang, Tuersuntuheti Amanisa, Junyi Zhu, Lijun Bao, Tingxin Shi, Meitong Liu, Jielin Huang, Dexun Ji, Yuanhan Sui, Wenqi Zhu, Jie Shao, Shengchun Xu
