研究方向
研究兴趣包括RNA聚合酶亚基和三维功能基因组相关的基因表达调控机理。以早期胚胎干细胞和癌症细胞为模型，运用基因组学、蛋白质组学、生物信息学、计算机模拟、CRISPR基因编辑、光学成像和生物化学等多学科技术开展RNA聚合酶亚基调控的分子机理、动态变化和疾病的相关研究。主要致力于：
1. RNA聚合酶亚基新型功能的系统鉴定与分子机理研究
2. RNA聚合酶亚基与疾病
3. RNA聚合酶亚基相关的探针筛选
代表性科研论文
After 2016:
1. 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 Mar 14.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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).
7. 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.
8. 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).
9. 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).
10. 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.
11. 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.
12. 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.
13. 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.
14. 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:
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. Ji, X., and Fu, X.D. (2012). The mediator couples transcription and splicing. Molecular Cell 45, 433-434.
24. 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.
25. 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.
