Contact Information

Course Outlines

HSCI3004 Genomics and Bioinformatics

Advanced Molecular Cell Biology

Advanced Genetics and Bioinformatics

Research Team
Nitin NarwadeResearch AssistantN22-4001+853 8822
Yanying GUOResearch AssistantN22-4001+853 8822
Zhuoran GAOResearch AssistantN22-4001+853 8822
Lingling HUPhD StudentN22-4001+853 8822 2933
Guimei CUIPhD StudentN22-4001+853 8822 2933
Mi CHENPhD StudentN22-4001+853 8822 2933
Chao FANGPhD StudentN22-4001+853 8822 2933
Wei CAOPhD StudentN22-4001+853 8822 2933
Chen CHANGPhD StudentN22-4001+853 8822 2933
Yitian CHENPhD StudentN22-4001+853 8822 2933
Mokan DENGPhD StudentN22-4001+853 8822 2933
Yimin ZHENGPhD StudentN22-4001+853 8822 2933
Postdoctoral Research FellowDepartment of Molecular Biology and Genetics, Cornell University (1999-2004)
PhDMolecular Biology, School of Biological Sciences, Faculty of Science and Engineering, the University of Manchester (1995-2000)
BABiochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California, Berkeley (1988-1992)
2013-presentProfessor, Faculty of Health Sciences, University of Macau
2011-2013Adjunct Associate Professor, Department of Biochemistry, National
University of Singapore
2006-2011Adjunct Assistant Professor, Department of Biochemistry, National
University of Singapore
2006-2013Faculty, NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore
2006-2013Adjunct Assistant Professor, School of Biological Sciences, Nanyang Technological University
2004-2013Senior Investigator, Cancer Biology and Pharmacology, Genome
Institute of Singapore
1996-1998Graduate Research/Teaching Assistant, School of Biological Sciences, the University of Manchester
Research Interests
My lab is interested in understanding the molecular details of nuclear hormone signaling and how these pathways relate to disease conditions, including cancers. Currently, we are investigating how lipophilic hormones such as estrogens and androgens regulate the transcriptional activities of nuclear hormone receptors in the context of a chromatin environment. We employ a combination of powerful biological tools, including modern genetic and cell-based techniques (RNAi, ChIP, and FISH) and next-generation sequencing approaches (ChIP-Seq, RNA-Seq, and ChIA-PET), to define the molecular mechanisms of transcriptional regulation by estrogen and androgen receptors. The findings from our work will have direct impact towards the development of therapeutic targets for the wide range of diseases and disorders in which these and other nuclear receptors play a role.
Representative Publications
  • *Zhang, Z., *Chng, K. R., *Lingadahalli, S., Chen, Z., Liu, M. H., Guan, P., Do H. H., Cai, S., Rinaldi, N., Poh, H. M, Li, G., Sung, Y. Y., Heng, C. L., Core, L. J., Tan, S. K., Ruan, X., Lis, J. T., Kellis, M., Ruan, Y., Sung, W. K., and Cheung, E. (2018) An AR-ERG Transcriptional Signature Defined by Long Range Chromatin Interactomes in Prostate Cancer Cells. Genome Research (Accepted) *Equal contribution.
  • Zhu, D., Zhao, X., Cui, G., Chang, S., Hu, L., See, Y. X., Lim, G. M. L., Guo, D., Chen, X., Robson, P., Luo, Y., and Cheung, E. (2018) Single-Cell Transcriptome Analysis Reveals Estrogen Signaling Coordinately Augments One-Carbon, Polyamine, and Purine Synthesis in Breast Cancer. Cell Reports 25, 2285-2298
  • Lingadahalli, S., Jadhao, S., Sung, Y. Y., Chen, M., Hu, L., Chen, X., and Cheung, E. (2018) Novel lncRNA LINC00844 Regulates Prostate Cancer Cell Migration and Invasion Through AR Signaling. Molecular Cancer Research, doi: 10.1158/1541-7786.MCR-18-0087.
  • Chen, X., Miao, Z., Divate, M., Zhao, Z., and Cheung, E. (2018) KM-Express: An Integrated Online Patient Survival and Gene Expression Analysis Tool for the Identification and Functional Characterization of Prognostic Markers in Breast and Prostate Cancers. Database doi: 10.1093/database/bay069.
  • Divate, M. and Cheung, E. (2018) GUAVA: a Graphical User interface for the Analysis and Visualization of ATAC-seq data. Frontiers in Genetics, doi: 10.3389/fgene.2018.00250.
  • Hu, J., Tan, S. K., Lim, M. G. L., Chang, S. H., Cui, G., Liu, S., Narasimhan, K., New, S. Y., Wang, X., Chen, C., Chakravarty, H., Kolatkar, P. R., Tam, K., Qian, L., Su, X., Jauch, R., and Cheung, E. (2018) Identification of a Wells-Dawson Polyoxometalate-Based AP-2g Inhibitor with Pro-Apoptotic Activity. Biochemical Journal, 475: 1955-1977.
  • *Chen, X., Yang, C., Xie, S., and *Cheung, E. (2018) Long Non-coding RNAs GAS5 and ZFAS1 are Prognostic Markers Involved in Translation Targeted by miR-940 in Prostate Cancer. Oncotarget 9:1048-1062. *Co-corresponding authors.
  • Aung, K. M., Lim, M. G., Hong, S., *Cheung, E., and *Su, X. (2017) Determination of DNA Binding Behavior of FoxA1 Constructs Using a Gold Nanoparticle-Based High Throughput Assay. Journal of Molecular Engineering and Materials *Co-corresponding authors.
  • Liu, M. H. and Cheung, E. (2014) Estrogen Receptor-Mediated Long-Range Chromatin Interactions and Transcription in Breast Cancer. Molecular and Cellular Endocrinology 382, 624-632.
  • New, S. Y., Aung, K. M., Lim, M. G., Hong, S., Tan, S. K., Lu, Y., *Cheung, E., and *Su, X. (2014)
    Fast Screening of Ligand-Protein Interactions Based on Ligand-Induced Protein Stabilization of Gold Nanoparticles. Analytical Biochemistry 86, 2361-70. *Co-corresponding authors.
  • Aung, K. M., New, S. Y., Hong, S., Sutarlie, L., Lim, M. G., Tan, S. K., *Cheung, E., and *Su, X. (2014) Studying Forkhead Box Protein A1-DNA Interaction and Ligand Inhibition Using Gold Nanoparticles, Electrophoretic Mobility Shift Assay, and Fluorescence Anisotropy. Analytical Biochemistry 448, 95-104. *Co-corresponding authors.
  • Lukman, S., Aung, K. M., Lim, M. G., Hong, S., Tan, S. K., *Cheung, E., and *Su, X. (2014) Hybrid Assembly of DNA-Coated Gold Nanoparticles with Water Soluble Conjugated Polymers for Studying Protein-DNA Interaction and Ligand Inhibition. RSC Advances 4, 8883-8893. *Co-corresponding authors.
  • Sutarlie, L., Aung, K. M., Lim, M. G., Lukman, S., *Cheung, E., and *Su, X. (2014) Studying Protein-DNA Complexes using Gold Nanoparticles by Exploiting Particle Aggregation, Refractive Index Change, and Fluorescence Quenching and Enhancement Principles. Plasmonics doi: 10.1007/s11468-013-9655-2. *Co-corresponding authors.
  • Cheung, E. and Sun, Y. Y. (2013) Transcriptional Network of Castrate Resistant Prostate Cancer. Endocrine Related Cancer 21, R1-R11.
  • Sung, Y. Y., and Cheung, E. (2013) Antisense Now Makes Sense: Dual Modulation of Androgen-Dependent Transcription by CTBP1-AS. The EMBO Journal 12, 1653-1654.
  • Chng., K. R., and Cheung, E. (2012) Sequencing the Transcriptional Network of AR in Prostate Cancer. Cancer Letters 340, 254-260.
  • Chng, K. R., Chang, C. W., Tan, S. K., Yang, C., Hong, S. Z., Sng, N. Y. W., and Cheung, E. (2012) A Transcriptional Repressor Co-Regulatory Network Governing Androgen Response in Prostate Cancer. The EMBO Journal 31, 2810 – 2823.
  • Tan, P. Y., Chang, C. W., Chng, K. R., Abayratna, S., Sung, W. K., and Cheung, E. (2012)
    Integration of Regulatory Networks by NKX3.1 Promotes Androgen-Dependent Prostate Cancer Survival. Molecular and Cellular Biology 32, 399-414.
    #Highlighted as a hot article in the Spotlight section of MCB
  • Li, G., Ruan, X., Auerbach, R., Sandhu, K. S., Wang, P., Orlov, Y., Poh, H. M., Goh, Y., Lim, J., Sim, H. S., Peh, S. Q., Mulawadi, F. H., Ong, C. T., Landt, T., Raha, D., Euskirchen, G., Hong, S. Z., Thoreau, H., Wei, C. L., Ge, W., Sun, Y., Fullwood, M. J., Liu, E. T., Cheung, E., Sung, W. K., Snyder, M., and Yijun, R. (2012) Extensive Chromatin Interactions Provide Architectural Basis for Transcription Regulation in Eukaryotes. Cell 148, 84-98.
  • Tan, S. K., Lin, Z. H., Chang, C. W., Varang, V., Chng, K. R., Yong, E. L., Sung, W. K., and Cheung, E. (2011) AP-2 Regulates Oestrogen Receptor-Mediated Long-Range Chromatin Interaction and Gene Transcription. The EMBO Journal 30, 2569-81.
  • Zhang, Z. Z., Chang, C. W., Goh, W. L., *Sung, W. K., and *Cheung, E. (2011) CENTDIST: Discovery of Co-associated Factors by Motif Distribution. Nucleic Acid Research Suppl 2:W391-9. *Co-corresponding authors.
  • Cheung, E., and Ruan, Y. (2011) Determination of Transcription Factor Binding. Nature Genetics 43,1.
  • Huang, P. Y. H., Han, Y., Handoko, L., Velkov, S., Wong, E., Cheung, E., Ruan, X., Wei, C. L., Fullwood, M. J., and Ruan, Y. (2010) Protocol: Sonication-based Circular Chromosome Conformation Capture with Next-Generation Sequencing Analysis for the Detection of Chromatin Interactions. Nature Protocol Exchange doi:10.1038/protex.2010.207
  • Mason, C. E., Shu, F., Wang, C., Session, R. M., Kallen, R. G., Sidell, N., Yu, T., Liu, M. H., Cheung, E., Kallen, C. B. (2010) Location Analysis for the Estrogen Receptor-{alpha} Reveals Binding to Diverse ERE Sequences and Widespread Binding Within Repetitive DNA Elements. Nucleic Acid Research 38, 2355-68.
  • *Joseph, R., *Orlov, Y. L., *Huss, M., Sun, W., Ukil, L., Kong, S. L., Pan, Y. F., Li, G., Lim, M., Thomsen, J. S., Ruan, Y., Clarke, N.D., Prabhakar, S., Cheung, E., and Liu, E. T. (2010) Genomic Factors Determining Binding Site Selection by Estrogen Receptor α. *Equal contributions. Molecular Systems Biology 6:456
  • Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Xu, H., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Huang, P. Y. H., Chew, E. G. Y., Yao, P., Huang, H., Welboren, W-J., Han, Y., Ooi, H. S., Ariyaratne, P. N., Vega, V. B., Luo, Y., Tan, P. Y., Choy, P. Y., Abayratna, K. D. S., Zhao, B., Lim, K. S., Leow, S. C., Yow, J. S., Joseph, R., Li, H., Desai, K. V., Thomsen, J. S., Lee, Y. K., Karuturi, R. K. M., Herve, T., Bourque, G., Stunnenberg, H. G., Ruan, X., Cacheux-Rataboul, V., Sung, K. W. K., Liu, E. T., Wei, C. L., *Cheung, E., and *Ruan, Y. (2009) An Oestrogen Receptor α-Bound Human Chromatin Interactome. Nature 482 (7269), 58-64. *Co-corresponding authors.
  • Pan, Y. F., Abayratna, S., Liu, M. H., Zhao, B., Hong, S. Z., Tan, P. Y., Lim, K. S., Bourque, G., Liu, E. T., and Cheung, E. (2008) Regulation of Estrogen Receptor-Mediated Long Range Transcription Via Evolutionarily Conserved Distal Response Elements. The Journal of Biological Chemistry 283, 32977-88.
  • Lin, C. Y., Vega, V. B., Thomsen, J. S., Zhang, T., Kong, S. L., Xie, M., Chiu, K. P., Lipovich, L., Barnett, D. H., Stossi, F., Yeo, A., George, J., Kuznetsov, V. A., Lee, Y. K., Charn, T. H., Palanisamy, N., Miller, L. D., Cheung, E., Katzenellenbogen, B. S., Ruan, Y., Bourque, G., Wei, C. L., and Liu, E. T. (2007) Whole-genome Cartography of Estrogen Receptor  Binding Sites. PLoS Genetics 3, e87.
  • Ross, S.*, Cheung, E.*, Petrakis, T.G., Howell, M., Kraus, W. L., and Hill, C. S. (2006) Smads Orchestrate Specific Histone Modifications and Chromatin Remodeling to Activate Transcription. *Equal Contributions. The EMBO Journal 25, 4490-4502.
  • Cheung, E., Acevedo, M. L., Cole, P. A., and Kraus, W. L.  (2005) Altered Pharmacology and Distinct Coactivator Usage for Estrogen Receptor-Dependent Transcription Through Activating Protein-1.  Proceedings of the National Academy of Sciences 102, 559-64.
  • Cheung, E., Schwabish, M. A., and Kraus, W. L.  (2003) Chromatin Exposes Intrinsic Differences in the Transcriptional Activities of Estrogen Receptors a and b.  The EMBO Journal 22, 600-11.
  • Cheung, E., Zarifyan, A. S., and Kraus, W. L.  (2002) Histone H1 Represses Estrogen Receptor Alpha Transcriptional Activity by Selectively Inhibiting Receptor-Mediated Transcription Initiation.  Molecular Cellular Biology 22, 2463-71.

*Co-corresponding authors

Research Grants
2018-2021University of Macau MYRG (MOP1,500,000: PI)
2016-2019FDCT Research Grant (MOP1,616,900: PI)
2015-2016FDCT Special Equipment Fund (MOP6,750,000: PI)
2015-2018University of Macau MYRG (MOP2,400,000: PI)
2015-2018FDCT Research Grant (MOP2,600,000: PI)
2014-2015University of Macau SRG (MOP150,000: PI)
2012-2015A*STAR Joint Council Office Grant, Integrative Analysis of the Oncogenic Transcription Factor, AP-2gamma, in Breast Cancer Using Nanobiotechnology and Genome Biology, (SGD$1,000,000, Project Director/PI)
2011-2014NMRC IRG, Novel Anti-Androgens of Botanical Origin as Multiple-Site Modulators of Androgen Receptor Signalling to Inhibit Prostate Cancer Development and Growth, (SGD$849,622, Co-PI)
2011-2013A*STAR-NZ HRC JGC Grant, Oestrogen-Dependent Regulation of Gene Expression by Cohesion in Breast Cancer, (SGD$250,000, Co-PI)
2008-2011A*STAR BMRC Grant, Molecular Mechanisms of Action and Human Bioaccumulation of a Novel Estrogenic Compound Secreted by a Singapore Phytoplankton Isolate, Chattonella marina, (S$604,132, Co-PI)
2013201303835-1: A method to screen small ligands and determine protein-ligand interactions (filed)
2013201303638-9: A hybrid sensor using metal nanoparticles and conjugated polymers (filed)
201213/651,141: Method of modulating a prostate cancer cell (filed)
2003-2004NIH NRSA Postdoctoral Fellowship
2000-2003Susan G. Komen Breast Cancer Foundation Postdoctoral Fellowship
1996-1998Overseas Research Studentship Award
1995-1998Frederick Craven Moore Research Studentship Award
Professional Activities
2013-presentEditorial Board, Molecular Cancer Research
Conference Presentations

  1. Cheung, E. EMBL Symposium: Cellular Heterogeneity, “Transcriptome Analysis of Androgen Signaling in Individual Prostate Cancer Cells”2015