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 genomics, proteomics, bioinformatics, genome editing, imaging and biochemistry techniques. Specific research direction includes:
1) Investigating the molecular mechanisms for chromatin interactions connecting
enhancers, promoters and insulators.
2) Understanding the dynamics of chromatin interactions among transcrIption regulatory elements and how they drive selective gene expression.
3) Identifying development and disease associated functional transcrIption regulatory elements and their regulation mechanisms.
Representative Peer-Reviewed Publications
1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. Wang, Y., Jiang, L., Ji, X., Yang, B., Zhang, Y., and Fu, X.D. (2013). Hepatitis B viral RNA directly mediates down-regulation of the tumor suppressor microRNA miR-15a/miR-16-1 in hepatocytes. The Journal of biological chemistry 288, 18484-18493.
8. Mo, S., Ji, X., and Fu, X.D. (2013). Unique role of SRSF2 in transcription activation and diverse functions of the SR and hnRNP proteins in gene expression regulation. Transcription 4, 251-259.
9. Ji, X., and Fu, X.D. (2012). The mediator couples transcription and splicing. Molecular Cell 45, 433-434.
10. 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.
11. 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.
History of modern molecular biology