Faculty

Education

2008-2013, Ph.D.
Department of Biochemistry and Molecular Biology
Wuhan University

2009-2012, Visiting graduate student
Department of Cellular and Molecular Medicine
UC, San Diego

2004-2008, B.S. Biological Science
Wuhan University

Professional Experience

2013-2016, Postdoc
Whitehead Institute for Biomedical Research, MIT

2016-, Associate Professor
School of Life Sciences
Peking-Tsinghua Center for Life Sciences
Peking University

Editorial Activities

2024-, Genome Biology, Editorial Board Member

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 computation theory, genomics, proteomics, bioinformatics, genome editing, imaging and biochemistry techniques. Specific research direction includes:
1）RNA polymerase related molecular mechanisms, diseases and probes
2）Biomolecular computing models and design

Representative Peer-Reviewed Publications

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.

Teaching

History of Modern Molecular Biology
Nuclear Structure and Function