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E-mail: xiongji(AT)pku.edu.cn
Lab Address: LUI CHE WOO BUILDING,Peking University, No.5 Yiheyuan Road, Haidian District,Beijing, P.R.China 100871
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Research Interests
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 genomics, proteomics, bioinformatics, genome editing, imaging and biochemistry techniques. Specific research direction includes:
1) Investigating the molecular mechanisms for the novel functions of RNA polymerase subunits.
2) Understanding the roles of RNA polymerase subunits in human brain diseases.
3) Screening RNA aptamers for RNA polymerase subunits.
Representative Peer-Reviewed Publications
After 2016:
1. 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. In press.
2. 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.
3. 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.
4. 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).
5. 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.
6. 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).
7. 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).
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.

Before 2016:
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. Ji, X., and Fu, X.D. (2012). The mediator couples transcription and splicing. Molecular Cell 45, 433-434.
22. 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.
23. 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.
History of Modern Molecular Biology
Nuclear Structure and Function
Laboratory Introduction