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

1. Activated transcriptional elongation and RNA stability of GPCR ligand binding genes unveiled via RNA polymerase II degradation. Bao, L., Zhu, J., Shi, T., Jiang, Y., Li, B., Huang, J.*, Xiong Ji*. Nucleic Acids Research. In press.
2. Subcellular localization shapes the fate of RNA polymerase III. Tian, K, Wang, R., Huang, J., Wang, H., Ji, X. *. Cell Reports. 2023 Aug 29;42(8):112941.
3. 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 Research. 2023 Jul 21;51(13):6784-6805.
4. 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.
5. Huang, J.*, Ji, X.*, Never a dull enzyme, RNA polymerase II. Transcription. Transcription. 2023 Nov;14(1-2):49-67.
6. 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.
7. Li, Y., Huang, J., Bao, L., Zhu, J., Duan, W., Zheng, H., Wang, H., Jiang, Y., Zhang, M., Yi, C., Ji, X.*. Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits. Molecular Cell. 2023 Apr 20;83(8):1280-1297.
8. 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).
9. 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.
10. 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.
11. 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.
12. 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).
13. 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.
14. 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.
15. Yang, B., Li, B., Jia, Li., Wang, X., Jiang, Y., Ji, X.*, Yang, P.*, 3D Landscape of Hepatitis B Virus with The Chromatin of Human Cells. Cell Discovery. 2020 Dec 29;6(1):95.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. Ji, X., and Fu, X.D. (2012). The mediator couples transcription and splicing. Molecular Cell. 45, 433-434.
26. 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.
27. 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.

季雄课题组长期从事RNA聚合酶非经典功能调控研究。主要集中在RNA聚合酶亚基未知功能调控、分子探针和生物计算等方向，近5年成果发表在Cell（2023）、Molecular Cell（2022，2023）、Genome Biology（2020，2022）、Nature Communications （2022）、Nucleic Acids Research (2023，2024)、Cell Reports (2023)、Cell Discovery （2020）、CMLS（2022）、iScience（2022）、Transcription (2023)、STAR Protocol（2023a, 2023b）等杂志上，为选择性基因表达调控提供新的假说。现因发展需要，招聘博士后1-2名。

History of Modern Molecular Biology
Nuclear Structure and Function

Laboratory Introduction