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

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，威人斯尼平台注册
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

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

杂志任职:

2024-，Genome Biology, 编委（Editorial Board Member）

执教课程:

近代分子生物学史话
细胞核的结构与功能

      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. Zheng, H., et al., CTDP1 and RPB7 stabilize Pol II and permit reinitiation. Nat Commun, 2025. 16(1): p. 2161.
2. Bao, L., et al., Increased transcriptional elongation and RNA stability of GPCR ligand binding genes unveiled via RNA polymerase II degradation. Nucleic Acids Res, 2024. 52(14): p. 8165-8183.
3. Liu, Y., et al., Fork coupling directs DNA replication elongation and termination. Science, 2024. 383(6688): p. 1215-1222.
4. Tian, K., et al., Subcellular localization shapes the fate of RNA polymerase III. Cell Rep, 2023. 42(8): p. 112941.
5. Wang, R., et al., Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res, 2023. 51(13): p. 6784-6805.
6. Huang, J., et al., Protocol for quantitative analysis of RNA 3'-end processing induced by disassociated subunits using chromatin-associated RNA-seq data. STAR Protoc, 2023. 4(3): p. 102356.
7. Huang, J. and X. Ji, Never a dull enzyme, RNA polymerase II. Transcription, 2023. 14(1-2): p. 49-67.
8. Wang, H., R. Zhou, and X. Ji, Droplet formation assay for investigating phase-separation mechanisms of RNA Pol II transcription and CTCF functioning. STAR Protoc, 2023. 4(2): p. 102202.
9. Li, Y., et al., RNA Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits. Mol Cell, 2023. 83(8): p. 1280-1297 e11.
10. Qin, F., et al., Linking chromatin acylation mark-defined proteome and genome in living cells. Cell, 2023. 186(5): p. 1066-1085 e36.
11. Jiang, Y., et al., Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture. Genome Biol, 2022. 23(1): p. 246.
12. Wang, H., et al., The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors. Nat Commun, 2022. 13(1): p. 5703.
13. Zhou, R., et al., CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions. iScience, 2022. 25(9): p. 105011.
14. Li, Y., et al., Targeted protein degradation reveals RNA Pol II heterogeneity and functional diversity. Mol Cell, 2022. 82(20): p. 3943-3959 e11.
15. Wang, C., et al., BRD2 interconnects with BRD3 to facilitate Pol II transcription initiation and elongation to prime promoters for cell differentiation. Cell Mol Life Sci, 2022. 79(6): p. 338.
16. Cao, L., et al., SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs. PLoS Pathog, 2022. 18(6): p. e1010599.
17. Xie, X., et al., C-terminal deletion-induced condensation sequesters AID from IgH targets in immunodeficiency. EMBO J, 2022. 41(11): p. e109324.
18. Liu, Y., et al., Transcription shapes DNA replication initiation to preserve genome integrity. Genome Biol, 2021. 22(1): p. 176.
19. Yang, B., et al., 3D landscape of Hepatitis B virus interactions with human chromatins. Cell Discov, 2020. 6(1): p. 95.
20. Jiang, Y., et al., Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III. Genome Biol, 2020. 21(1): p. 158.
21. Zhang, H., et al., Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci China Life Sci, 2020. 63(7): p. 953-985.
22. Huang, J., et al., BAT Hi-C maps global chromatin interactions in an efficient and economical way. Methods, 2020. 170: p. 38-47.
23. Liu, X.S., et al., Editing DNA Methylation in the Mammalian Genome. Cell, 2016. 167(1): p. 233-247 e17.
24. Ji, X., et al., 3D Chromosome Regulatory Landscape of Human Pluripotent Cells. Cell Stem Cell, 2016. 18(2): p. 262-75.
25. Sigova, A.A., et al., Transcription factor trapping by RNA in gene regulatory elements. Science, 2015. 350(6263): p. 978-81.
26. Ji, X., et al., Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions. Proc Natl Acad Sci U S A, 2015. 112(12): p. 3841-6.
27. Fong, N., et al., Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev, 2014. 28(23): p. 2663-76.
28. Mo, S., X. Ji, and X.D. Fu, Unique role of SRSF2 in transcription activation and diverse functions of the SR and hnRNP proteins in gene expression regulation. Transcription, 2013. 4(5): p. 251-9.
29. Ji, X., et al., SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell, 2013. 153(4): p. 855-68.
30. Wang, Y., et al., Hepatitis B viral RNA directly mediates down-regulation of the tumor suppressor microRNA miR-15a/miR-16-1 in hepatocytes. J Biol Chem, 2013. 288(25): p. 18484-93.
31. Ji, X. and X.D. Fu, The mediator couples transcription and splicing. Mol Cell, 2012. 45(4): p. 433-4.
32. Han, J., et al., Pre-mRNA splicing: where and when in the nucleus. Trends Cell Biol, 2011. 21(6): p. 336-43.
33. Xue, Y., et al., Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell, 2009. 36(6): p. 996-1006.
34. Ji Xiong, H.J., Zhu Junyi, Duan Wenjia, Li Yuanjun, Bao Lijun, , Meet the authors: The Ji lab. Molecular Cell, 2023. 83: p. 8.