Contact
Programs
Zhijie (Jason) Liu, Ph.D.
Associate Professor, Molecular Medicine
Different signals, including hormones, inflammatory cytokines and metabolic signals, work in a collaborative way to regulate context-specific gene programs in normal growth and disease conditions. However many questions are still open: How do these different signals crosstalk with each other for a specific gene expression program? How do signals affect the composition and organization of transcriptional machinery including transcription factors and their cofactors? How are epigenetic alterations and chromatin 3D architectural changes achieved in response to signals?
Dr. Jason Liu’s research is to understand how signal-dependent gene programs are regulated in cell differentiation/dedifferentiation and in the development of cancer and other diseases. Currently, his lab is combining biochemical, cellular, and animal model-related studies with different NGS-based assays to work on the following projects to understand gene regulation mechanisms and find their connection to clinical applications:
(1) Explore the roles and regulation mechanisms of signaling-dependent gene regulation programs in normal development and disease conditions, and study how context-specific gene programs are regulated by the crosstalk of different signaling pathways.
(2) Decipher the epigenetic and 3D architectural changes of the cis-regulatory elements upon developmental/pathological stimuli and during hormone/drug resistance acquisition in cancers.
(3) Based on our understanding of gene regulation mechanisms, identify diagnostic/prognostic biomarkers and therapeutic targets for multiple human cancer types.
(4) Develop drugs and therapeutics for pre-clinical studies and potential clinical applications.
Publications
1. Mingjun Bi, Zhao Zhang, Yi-Zhou Jiang, Pengya Xue, Hu Wang, Zhao Lai, Xiaoyong Fu, Carmine De Angelis, Yue Gong, Zhen Gao, Jianhua Ruan, Victor X. Jin, Elisabetta Marangoni, Elodie Montaudon, Christopher K. Glass, Wei Li, Tim H.M. Huang, Zhi-Ming Shao, Rachel Schiff, Lizhen Chen*, Zhijie Liu*. Enhancer Reprogramming Driven by High-order Assemblies of Transcription Factors Promotes Phenotypic Plasticity and Breast Cancer Endocrine Resistance**. Nature Cell Biology. 2020 Jun; 22(6):701-715. PMID: 32424275 (*co-corresponding author).
**Featured as a “News and Views” in Nature Cell Biology: Wu X, Vakoc C. A pliable ERα cistrome evades therapy. Nature Cell Biology. 2020 Jun; 22(6):619-620. PMID: 32424274
2. Zhao Zhang, Wei Yu, Dan Tang, Yufan Zhou, Mingjun Bi, Hu Wang, Yan Zheng, Mingqiu Chen, Li Li, Xinping Xu, Wei Zhang, Huimin Tao, Victor X. Jin, Zhijie Liu*, and Lizhen Chen *. Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer. RNA Biology. 2020 Jun 7 Published online PMID: 32506995 (*co-corresponding author)
4. Nahim Adnan, Zhijie Liu, Tim H.M. Huang, and Jianhua Ruan. Comparative evaluation of network features for the prediction of breast cancer metastasis. BMC Medical Genomics. 2020 Apr 13: 40. PMID: 32241278
3. Su Hyuk Ko, Ellen Apple, Zhijie Liu*, Lizhen Chen*. Age-dependent autophagy induction after injury promotes axon regeneration via limiting Notch. Autophagy. 2020 Jan 13:1-17. PMID: 31920157 (*co-corresponding author)
5. Lizhen Chen* and Zhijie Liu*. Multifaceted function of YAP/TEAD on chromatin: prospects of 'A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer'. J Mol Cell Biol. 2019 Dec 19;11(12):1101-1103. PMID: 31774121 (*co-corresponding author)
6. Chi Zhu, Li Li, Zhao Zhang, Mingjun Bi, Hu Wang, Wenyue Su, Karen Hernandez, Pingping Liu, Junqiang Chen, Mingqiu Chen, Tim Hui-Ming Huang, Lizhen Chen, and Zhijie Liu*. A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer. Molecular Cell. 2019 Aug 22;75(4):791-806. PMID: 31303470 (*lead author)
7. Joshua E Mayfield, Seema Irani, Edwin E Escobar, Zhao Zhang, Nathaniel T Burkholder, Michelle R Robinson, M Rachel Mehaffey, Sarah N Sipe, Wanjie Yang, Nicholas A Prescott, Karan Kathuria, Zhijie Liu, Jennifer Brodbelt, Yan Zhang. Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb. eLife. 2019 Aug 6; doi: 10.7554/eLife.48725. PMID: 31385803
8. Shiyan Wang, Jiahuan Chen, Sara P. Garcia, Xiaodong Liang, Fang Zhang, Pengyi Yan, Huijing Yu, Weiting Wei, Zixuan Li, Jingfang Wang, Huangying Le, Zeguang Han, Xusheng Luo, Daniel S. Day, Sean M. Stevens, Yan Zhang, Peter J. Park, Zhijie Liu, et al., and Bing Zhang. A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA. Genome Research. 2019 Feb; 29(2):193-207. PMID: 30670628
9. Aiping Xu, Zhao Zhang, Su‐Hyuk Ko, Alfred L. Fisher, Zhijie Liu, Lizhen Chen. Microtubule regulators regulate neuronal aging and organismal longevity through DAF-16 in C. elegans. Aging Cell. 2019 Jan 14:e12884. PMID: 30638295
10. Aaron M. Horning, Yao Wang, Che-Kuang Lin, Anna D. Louie, Rohit R. Jadhav, Chia-Nung Hung, Chiou-Miin Wang, Chun-Lin Lin, Nameer B. Kirma, Michael A. Liss, Addanki P. Kumar, LuZhe Sun, Zhijie Liu, Wei-Ting Chao, Qianben Wang, Victor X. Jin, Chun-Liang Chen and Tim H.-M. Huang. Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle–Related Transcription and Attenuated Androgen Response. Cancer Research. 2018 Feb 15; 78 (4): 853-864. PMID: 29233929
11. Feng Yang, Qi Ma, Zhijie Liu, Wenbo Li, Yuliang Tan, Chunyu Jin, Wubin Ma, Yiren Hu, Jia Shen, Kenneth A. Ohgi, Francesca Telese, Wen Liu and Michael G. Rosenfeld. Glucocorticoid Receptor: MegaTrans Switching Mediates the Repression of an ERα-Regulated Transcriptional Program. Molecular Cell. 2017 May 4;66(3):321-331. PMID: 28475868
12. Lizhen Chen, Zhijie Liu, Bing Zhou, Chaoliang Wei, Yu Zhou, Michael G. Rosenfeld, Xiangdong Fu, Andrew D. Chisholm, and Yishi Jin. CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of syntaxins. eLife. 2016 Jun 2; doi: 10.7554/eLife.16072. PMID: 27253061
13. Jianxun Wang, Francesca Telese, Yuliang Tan, Wenbo Li, Chunyu Jin, Xin He, Harihar Basnet, Qi Ma, Daria Merkurjev, Xiaoyan Zhu, Zhijie Liu, et al., and Michael G. Rosenfeld. LSD1n is an H4K20 demethylase regulating memory formation via transcriptional elongation control. Nature Neuroscience. 2015 Sep; 18(9): 1256-1264. PMID: 26214369
14. Wenbo Li, Yiren Hu, Soohwan Oh, Qi Ma, Daria Merkurjev, Xiaoyuan Song, Xiang Zhou, Zhijie Liu, et al., and Michael G. Rosenfeld. Condensin I and II complexes license full estrogen receptor α-dependent enhancer activation. Molecular Cell. 2015 Jul 16; 59(2): 188–202. PMID: 26166704
15. Feng Zhang, Bogdan Tanasa, Daria Merkurjev, Chijen Lin, Xiaoyuan Song, Wenbo Li, Yuliang Tan, Zhijie Liu, et al., and Michael G. Rosenfeld. Enhancer-bound LDB1 regulates a corticotrope promoter pausing repression program. PNAS. 2015 Feb 3; 112(5): 1380-5. PMID: 25605944
16. Janusz Puc, Piotr Kozbial, Wenbo Li, Yuliang Tan, Zhijie Liu, Tom Suter, Kenneth A. Ohgi, Jie Zhang, Aneel K. Aggarwal, and Michael G. Rosenfeld. Ligand-dependent enhancer activation requires topoisomerase-I catalytic activity. Cell. 2015 Jan 29; 160(3): 367-80. PMID: 25619691
17. Zhijie Liu*, Daria Merkurjev, Feng Yang, Wenbo Li, et al., and Michael G. Rosenfeld. Enhancer activation requires trans-recruitment of a mega transcription factor complex. Cell. 2014 Oct 9; 159(2): 358-73. PMID: 25303530 (*first and co-corresponding author)
18. Zhijie Liu*, Qidong Hu, and Michael G. Rosenfeld. Complexity of the RAR-mediated transcriptional regulatory programs. Chapter 10 of Book “The biochemistry of retinoic acid receptors I: structure, activation, and function at the molecular Level”. Subcellular Biochemistry. 2014; 70: 203-225. PMID: 24962887 (*first and co-corresponding author)
19. Dorota Skowronska-Krawczyk, Qi Ma, Michal Schwartz, Kathleen Scully, Wenbo Li, Zhijie Liu, et al., and Michael G. Rosenfeld. Required interactions of enhancers with Matrin-3 nuclear architecture for transcriptional activation by homeodomain factors. Nature. 2014 Aug 3; 514(7521): 257-61. PMID: 25119036
20. Kaitlin A. G. Reeh, Kim T. Cardenas, Virginia E. Bain, Zhijie Liu, Micheline Laurent, Nancy R. Manley and Ellen R. Richie. Ectopic TBX1 suppresses thymic epithelial cell differentiation and proliferation during thymus organogenesis. Development. 2014 Aug; 141(15): 2950-8. PMID: 25053428
21. Jie Li, Zhijie Liu, Shiyun Xiao and Nancy Manley. Transdifferentiation of parathyroid cells into cervical thymi promotes atypical T cell development. Nature Communications. 2013 Dec 17; 4:2959. PMID: 24343363
22. Zhijie Liu, Alison Farley, Lizhen Chen, Beth J. Kirby, Christopher S. Kovacs, C. Clare Blackburn, Nancy Manley. Thymus-associated parathyroid hormone has two cellular origins with distinct endocrine and immunological functions. PLoS Genetics. 2010 Dec 23; 6(12):e1001251. PMID: 21203493
23. Zhijie Liu, Shannon Yu, Nancy Manley. Gcm2 is required for the differentiation and survival of parathyroid precursor cells in parathyroid/thymus primordia. Developmental Biology. 2007 May 1; 305(1): 333-46. PMID: 17382312
24. Cunlan Liu, Fumi Saito, Zhijie Liu, Yu Lei, Shoji Uehara, Paul Love, Martin Lipp, Shunzo Kondo, Nancy Manley, and Yousuke Takahama. Coordination between CCR7- and CCR9-mediated chemokine signals in prevascular fetal thymus colonization. Blood. 2006 Oct 15; 108(8): 2531-9. PMID: 16809609
25. W. Li, Y. Wan, Z. Liu, K. Liu, X. Liu, B. Li, Z. Li, X. Zhang, Y. Dong, D. Wang. Molecular characterization of HMW glutenin subunit allele 1Bx14: further insights into the evolution of Glu-B1-1 alleles in wheat and related species. Theoretical and Applied Genetics. 2004; 109: 1093-1104. PMID:15290043
26. Liu Zhijie, Yan Zehong, Wan Yongfang, Liu Kunfan, Zheng Youliang, Wang Daowen. Analysis of HMW glutenin subunits and their coding sequences in two diploid Aegilops species. Theoretical and Applied Genetics. 2003; 106: 1368-1378. PMID: 12750780
27. Liu Zhijie, Zhang Xuemin, Wan Yongfang, Liu Kunfan, Wang Daowen. Characterization of high-molecular-weight glutenin subunits and their coding genes from Aegilops umbellulata. Acta Botanica Sinica. 0577-7496 2002; 44(7): 809-814.
28. Feng Hu-yuan, Xu Shi-jian, An Li-Zhe, Liu Zhi-Jie, Wang Xun-ling. Effects of increased UV-B radiation on seed germination and seedlings growth of eight cultivars of Glycine max. Acta Botanica Boreali-Occidentalia Sinica. 2001; 21(1).
Grants
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Private |
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| Funding Agency | The V Foundation for Cancer Research |
| Title | Functional and Architectural Studies of ERI? Enhancer in Breast Cancer Hormone Resistance |
| Status | Active |
| Period | 11/2016 - 11/2018 |
| Role | Principal Investigator |
| Grant Detail | |
State |
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| Funding Agency | School of Medicine UTHSCSA |
| Title | School of Medicine Translational Women?s Health Research Program |
| Status | Active |
| Period | 8/2016 - 8/2017 |
| Role | Principal Investigator |
| Grant Detail | |
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| Funding Agency | CPRIT |
| Title | CPRIT Award for the First-Time, Tenure-Track Faculty Members |
| Status | Active |
| Period | 3/2016 - 2/2020 |
| Role | Principal Investigator |
| Grant Detail | |
| Funding Agency | UTHSCSA PUF Funds |
| Title | UT Rising STARs Award |
| Status | Active |
| Period | 2/2016 - 2/2017 |
| Role | Principal Investigator |
| Grant Detail | |
Education
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| Year | Degree | Discipline | Institution |
| 2016 | Postdoctoral Training | The Howard Hughes Medical Institute, University of California at San Diego, CA | |
| 2008 | Postdoctoral Training | University of Georgia, Athens, GA | |
| 2007 | PhD | Genetics | University of Georgia, Athens, GA |
| 2002 | MS | Molecular Genetics | Chinese Academy of Sciences Beijing, China |
| 1999 | BS | Biochemistry | Lanzhou University Lanzhou, Gansu, China |