Education
2008-2013, Ph.D.
Department of Biochemistry and Molecular Biology
Wuhan University
2009-2012, Visiting graduate student
Department of Cellular and Molecular Medicine
UC, San Diego
2004-2008, B.S. Biological Science
Wuhan University
Professional Experience
2013-2016, Postdoc
Whitehead Institute for Biomedical Research, MIT
2016-, Associate Professor
School of Life Sciences
Peking-Tsinghua Center for Life Sciences
Peking University
Editorial Activities
2024-, Genome Biology, Editorial Board Member
Teaching
History of Modern Molecular Biology
Nuclear Structure and Function
Research interests focus on the mechanisms of gene expression regulation related to RNA polymerases. Using early embryonic stem cells and cancer cells as models, multidisciplinary approaches—including genomics, proteomics, bioinformatics, computational modeling, theoretical computation, CRISPR gene editing, optical imaging, and biochemistry—are employed to investigate the principles of gene expression regulation. Primary efforts are dedicated to:
1. Molecular mechanisms, diseases, and therapies associated with RNA polymerases.
2. Design of functional biomolecules.
1. Zhu J, Bao L, Xu S, Ji X*. FeaSion decodes the regulatory landscape and functional diversity of RNA polymerase II CTD phosphorylation. Science Advances. 2025 Nov 28;11(48): eadz2345.
2. Shao C, Hao Y, Jiang L, Wang D, Wang R, Li Y, Wang H, Ge Y, Bai R, Du X, Chen X, Wu T, Gou LT, Wan R, Xu Y, Ji X, Fu XD. Dynamic U2AF cycling defines two phases of cotranscriptional pre-mRNA splicing. Science. 2025 Sep 25;389(6767): eadj9141.
3. Liu M, Xu Q, Wang H*, Ji X*. INO80/SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape. Nucleic Acids Res. 2025 Sep 5;53(17): gkaf892.
4. Zheng H, Xu Q, Ji D, Yang B, Ji X*. CTDP1 and RPB7 stabilize Pol II and permit reinitiation. Nature Communications. 2025 Mar 4;16(1): 2161.
5. Bao L, Zhu J, Shi T, Jiang Y, Li B, Huang J*, Ji X*., Increased transcriptional elongation and RNA stability of GPCR ligand binding genes unveiled via RNA polymerase II degradation. Nucleic Acids Res. 2024 Aug 12;52(14):8165-8183.
6. Liu Y, Zhangding Z, Liu X, Gan T, Ai C, Wu J, Liang H, Chen M, Guo Y, Lu R, Jiang Y, Ji X., Gao N, Kong D, Li Q, Hu J.*, Fork coupling directs DNA replication elongation and termination. Science. 2024 Mar 15;383(6688):1215-1222.
7. Huang, J.*, Ji, X.*, Never a dull enzyme, RNA polymerase II. Transcription. 2023 Nov;14(1-2):49-67.
8. Tian K, Wang R, Huang J, Wang H, Ji, X.*, Subcellular localization shapes the fate of RNA polymerase III. Cell Reports. 2023 Aug 29;42(8):112941.
9. Wang, R., Xu, Q., Wang, C., Tian, K., Wang, H., Ji, X.*. Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res. 2023 Jul 21;51(13):6784-6805.
10. Huang J. *, Bao L., Zhu J., Ji, X.*, Protocol for quantitative analysis of RNA 3'-end processing induced by disassociated subunits using chromatin-associated RNA-seq data. STAR protocol. 2023 Jun 15;4(3):102356.
11. Li, Y., Huang, J., Bao, L., Zhu, J., Duan, W., Zheng, H., Wang, H., Jiang, Y., Liu, W., Zhang, M., Yu, Y., Yi, C., Ji, X.*, Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits. Molecular Cell. 2023 Apr 20;83(8):1280-1297.
12. Ji X., Huang J., Zhu J., Duan W., Li Y., Bao L., Meet the authors: The Ji lab. Molecular Cell. 2023 Apr 20;83(8):1197-1199.
13. Wang, H.*, Zhou R., Ji, X.*, Droplet formation assay for investigating phase-separation mechanisms of RNA Pol II transcription and CTCF functioning. STAR protocol. 2023 Mar 28;4(2).
14. 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.*. Linking chromatin acylation mark-defined proteome and genome in living cells. Cell. 2023 Mar 2; 186(5):1066.
15. Jiang, Y., Huang, J., Tian, K., Zheng, H., Zhu, Y., Guo, T., Ji, X.*. Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture. Genome Biology. 2022 Nov 28;23(1):246.
16. 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.*, The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors. Nature Communications. 2022 Sep 28;13(1):5703.
17. Zhou, R., Tian, K., Huang, J., Duan, W., Fu, H., Feng, Y., Wang, H., Jiang, Y., Li, Y., Wang, R., Hu, J., Ma, H., Qi, Z.*, Ji X.*, CTCF DNA binding domain undergoes dynamic and selective protein–protein interactions. iScience. 2022 Sep 16; 25(9).
18. 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.*, Targeted protein degradation reveals Pol II heterogeneity and functional diversity. Molecular Cell. 2022 Sep 9: S1097-2765(22)00812-7.
19. Wang, C., Xu, Q., Zhang, X., Day, D.S., Abraham, B.J., Lun, K., Chen, L., Huang, J.*, Ji, X.*, BRD2 interconnects with BRD3 to facilitate Pol II transcription initiation and elongation to prime promoters for cell differentiation. Cell Mol Life Sci. 2022 Jun 4;79(6):338.
20. Cao, L., Luo, Y., Guo, X., Liu, S., Li, S., Li, J., Zhang, Z., Zhao, Y., Zhang, Q., Gao, F., Ji, X., Gao, X., Li, Y., You, F., SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs. PLoS Pathog. 2022 Jun 3;18(6).
21. Xie, X., Gan, T., Rao, B., Zhang, W., Panchakshari, R.A., Yang, D., Ji, X., Cao, Y., Alt, F.W., Meng, F.L., Hu, J., C-terminal deletion-induced condensation sequesters AID from IgH targets in immunodeficiency. EMBO J. 2022 Jun 1;41(11).
22. Liu, Y., Ai, C., Gan, T., Wu, J., Jiang, Y., Liu, X., Lu, R., Gao, N., Li, Q., Ji, X., Hu, J. Transcription shapes DNA replication initiation to preserve genome integrity. Genome Biology. 2021 Jun 9;22(1):176.
23. Yang, B., Li, B., Jia, Li., Wang, X., Jiang, Y., Ji, X.*, Yang, P.*, 3D landscape of Hepatitis B virus interactions with human chromatins. Cell Discovery. 2020 Dec 29;6(1):95.
24. Jiang, Y., Huang, J., Lun, K., Li, B., Li, Y., Zheng, H., Li, Y., Zhou, R., Duan, W., Wang, C., Feng, Y., Yao, H., Li, C., Ji, X.*, Genome-wide Analyses of Chromatin Interactions After the Loss of Pol I, Pol II and Pol III. Genome Biology. 2020 Jul 2;21(1):158.
25. Zhang, H.*, Ji, X.*, Li, P.*, Liu, C.*, Lou, J.*, Wang, Z., Wen, W.*, Xiao, Y., Zhang, M.*, Zhu, X.*, Liquid-liquid Phase Separation in Biology: Mechanisms, Physiological Functions and Human Diseases. Science China Life Sciences. 2020 April 30.
26. Huang, J.*, Jiang, Y., Zheng, H., Ji, X.*, BAT Hi-C Maps Global Chromatin Interactions in An Efficient and Economical Way. Methods. 2020 Jan 1; 170: 38-47.
27. Ji, X., Dadon, D.B., Powell, B.E., Fan, Z.P., Borges-Rivera, D., Shachar, S., Weintraub, A.S., Hnisz, D., Pegoraro, G., Lee, T.I., et al. (2016). 3D Chromosome Regulatory Landscape of Human Pluripotent Cells. Cell Stem Cell. 18, 262-275.
28. Liu, X.S., Wu, H., Ji, X., Stelzer, Y., Wu, X., Czauderna, S., Shu, J., Dadon, D., Young, R.A., and Jaenisch, R. (2016). Editing DNA Methylation in the Mammalian Genome. Cell. 167, 233-247 e217.
29. Sigova, A.A., Abraham, B.J., Ji, X., Molinie, B., Hannett, N.M., Guo, Y.E., Jangi, M., Giallourakis, C.C., Sharp, P.A., and Young, R.A. (2015). TranscrIption factor trapping by RNA in gene regulatory elements. Science. 350, 978-981.
30. Ji, X., Dadon, D.B., Abraham, B.J., Lee, T.I., Jaenisch, R., Bradner, J.E., and Young, R.A. (2015). Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions. Proceedings of the National Academy of Sciences of the United States of America. 112, 3841-3846.
31. Fong, N., Kim, H., Zhou, Y., Ji, X., Qiu, J., Saldi, T., Diener, K., Jones, K., Fu, X.D., and Bentley, D.L. (2014). Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes & Development. 28, 2663-2676.
32. Wang, Y., Jiang, L., Ji, X., Yang, B., Zhang, Y., and Fu, X.D. (2013). Hepatitis B viral RNA directly mediates down-regulation of the tumor suppressor microRNA miR-15a/miR-16-1 in hepatocytes. The Journal of biological chemistry. 288, 18484-18493.
33. Mo, S., Ji, X., and Fu, X.D. (2013). Unique role of SRSF2 in transcription activation and diverse functions of the SR and hnRNP proteins in gene expression regulation. Transcription. 4, 251-259.
34. Ji, X., Zhou, Y., Pandit, S., Huang, J., Li, H., Lin, C.Y., Xiao, R., Burge, C.B., and Fu, X.D. (2013). SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell. 153, 855-868.
35. Han, J., Ji, X., Wang, D., and Fu, X.D. (2011). Pre-mRNA splicing: where and when in the nucleus. Trends in Cell Biology. 21, 336-343.
36. Ji, X., and Fu, X.D. (2012). The mediator couples transcription and splicing. Molecular Cell. 45, 433-434.
37. Xue, Y., Zhou, Y., Wu, T., Zhu, T., Ji, X., Kwon, Y.S., Zhang, C., Yeo, G., Black, D.L., Sun, H., et al. (2009). Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Molecular Cell. 36, 996-1006.
