教育經曆:

2008-2013，博士，生物化學與分子生物學，武漢大學
2009-2012，聯合培養博士，加州大學聖地亞哥分校
2004-2008，本科，生物技術，武漢大學

工作經曆:

2013-2016，博士後，麻省理工學院白頭生物醫學研究所
2016-現在，研究員，beat365官方网站
2016-現在，研究員，北大-清華生命科學聯合中心

榮譽獎勵:

2013, 吳瑞獎學金
2013, 湖北省優秀博士論文
2017, 億方學者
2017-2022, 國家重點研發計劃專項青年項目，首席科學家

學術任職:

2023-，中國細胞生物學會染色質生物學會委員
2023-，中國遺傳學會三維基因組學會委員

雜志任職:

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

執教課程:

近代分子生物學史話
細胞核的結構與功能

      研究興趣包括RNA聚合酶和分子計算相關的基因表達調控機理。以早期胚胎幹細胞和癌症細胞為模型，運用計算理論、基因組學、蛋白質組學、生物信息學、計算機模拟、CRISPR基因編輯、光學成像和生物化學等多學科技術開展基因表達調控中的生命分子計算原理研究。主要緻力于：
1. RNA聚合酶相關的分子機理、疾病與探針
2. 生命分子計算模型與設計

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.