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个人简历
教育经历
2008-2013，博士，生物化学与分子生物学，武汉大学
2009-2012，联合培养博士，加州大学圣地亚哥分校
2004-2008，本科，生物技术，武汉大学
2009-2012，联合培养博士，加州大学圣地亚哥分校
2004-2008，本科，生物技术，武汉大学
工作经历
2013-2016，博士后，麻省理工学院白头生物医学研究所
2016-现在，研究员，北京大学生命科学学院
2016-现在，研究员，北大-清华生命科学联合中心
2016-现在，研究员，北京大学生命科学学院
2016-现在，研究员，北大-清华生命科学联合中心
荣誉奖励
2013, 吴瑞奖学金
2013, 湖北省优秀博士论文
2017, 億方学者
2017-2022, 国家重点研发计划专项青年项目，首席科学家
2013, 湖北省优秀博士论文
2017, 億方学者
2017-2022, 国家重点研发计划专项青年项目，首席科学家
学术任职
2023-，中国细胞生物学会染色质生物学会委员
2023-，中国遗传学会三维基因组学会委员
2023-，中国遗传学会三维基因组学会委员
杂志任职
2024-，Genome Biology, 编委（Editorial Board Member）
科研领域描述
研究兴趣包括RNA聚合酶和分子计算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，运用计算理论、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基因表达调控中的生命分子计算原理研究。主要致力于：
1. RNA聚合酶相关的分子机理、疾病与探针
2. 生命分子计算模型与设计
1. RNA聚合酶相关的分子机理、疾病与探针
2. 生命分子计算模型与设计
代表性论文
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。
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。
执教课程
近代分子生物学史话
细胞核的结构与功能
细胞核的结构与功能
实验室简介
研究兴趣包括：RNA聚合酶 | 基因表达调控 | 转录调控 | 三维染色质结构 | 表观遗传 | 相分离
