Division of Life Science
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Danny Chi Yeu LEUNG

PhD University of British Columbia
Assistant Professor

Email: dcyleung@ust.hk

Division of Life Science, HKUST

Dr. Leung Research Laboratory Page

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Research Interests:


Mammalian genomes consist mostly of non-coding sequences. Within this massive proportion, previously misclassified as “junk DNA”, resides elements that function to regulate normal transcriptional programs. I am particularly interested in two classes of non-coding sequences: cis-regulatory elements (transcriptional promoters and enhancers) and endogenous retroviruses. The research of my laboratory focuses on dissecting how non-coding sequences are epigenetically regulated in both normal development and disease. We utilize various epigenomic and cell biology tools to delineate epigenetic pathways that modulate the activities of cis-regulatory elements and endogenous retroviruses, and their downstream effects on gene expression. Specially, I am interested in 1) elucidating the function of endogenous retroviruses in cellular differentiation during development; 2) determining the function of chromatin modifiers in progenitor and stem cells; and 3) uncovering the role of chromatin modifiers in melanomas.

Representative Publications:

  1. Angela D. Kelsey, Christine Yang, Danny Leung, Jakub Minks, Thomas Dixon-McDougall, Sarah E.L. Baldry, Aaron B. Bogutz, Louis Lefebvre and Carolyn J. Brown. Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST(2015) Genome Biology 16:208

  2. Danny Leung*, Inkyung Jung*, Nisha Rajagopal*, Anthony Schmitt, Siddarth Selvaraj, Ah Young Lee, Chia-An Yen, Shin Lin, Yiing Lin, Yunjiang Qiu, Wei Xie, Feng Yue, Manoj Hariharan, Pradipta Ray, Samantha Kuan, Lee Edsall, Hongbo Yang, Neil C. Chi, Michael Q. Zhang , Joseph R. Ecker, Bing Ren. Integrative analysis of haplotype-resolved epigenomes across human tissues (2015) Nature 518, 350–354 *-authors contributed equally

  3. Matthew D. Schultz, Yupeng He, John W. Whitaker, Manoj Hariharan, Eran A. Mukamel, Danny Leung, Nisha Rajagopal, Joseph R. Nery, Mark A. Urich, Huaming Chen, Shin Lin, Yiing Lin, Inkyung Jung, Anthony D. Schmitt, Siddarth Selvaraj, Bing Ren, Terrence J. Sejnowski, Wei Wang, Joseph R. Ecker. Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation (2015) Nature 518(7539):350-4
  4. Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. (2015) Nature 518: 317–330

  5. David U. Gorkin, Danny Leung and Bing Ren. The 3D Genome in Transcriptional Regulation and Pluripotency. (2014) Cell Stem Cell 14(6), 762–775

  6. Danny Leung, Tingting Du, Ulrich Wagner, Wei Xie, Ah Young Lee, Preeti Goyal, Yujing Li, Keith E. Szulwach, Peng Jin, Matthew Lorincz and Bing Ren. Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. (2014) PNAS volume 111 no.18: 6690-6695

  7. Wei Xie, Matt Schultz, Ryan Lister, Zhonggang Hou, Nisha Rajagopal, Pradipta Ray, John Whitaker, Shulan Tian, R. David Hawkins, Danny Leung, Hongbo Yang, Tao Wang, Ah Young Lee, Scott A. Swanson, Jiuchun Zhang, Yun Zhu, Audrey Kim, Joseph Nery, Mark A. Urich, Samantha Kuan, Chia-an Yen, Sarit Klugman, Pengzhi Yu, Kran Suknuntha, Nicholas E. Propson, Huaming Chen, Lee E. Edsall, Ulrich Wagner, Yan Li, Zhen Ye, Ashwinikumar Kulkarni, Zhenyu Xuan, Wen-yu Chung, Neil C. Chi, Jessica Antosiewicz-Bourget, Igor Slukvin, Ron Stewart, Michael Q. Zhang, Wei Wang, James A. Thomson, Joseph R. Ecker, and Bing Ren. Epigenomic analysis of multi-lineage differentiation of human embryonic stem cells. (2013) Cell, Volume 153, Issue 5, 1134-1148

  8. Alireza Baradaran-Heravi1, Kyoung Sang Cho, Bas Tolhuis, Mrinmoy Sanyal, Olena Morozova, Marie Morimoto, Leah I. Elizondo, Darren Bridgewater, Joanna Lubieniecka, Kimberly Beirnes, Clara Myung, Danny Leung, Hok Khim Fam, Kunho Choi, Yan Huang, Kira Y. Dionis, Jonathan Zonana, Kory Keller, Peter Stenzel, Christy Mayfield, Thomas Lücke, Arend Bokenkamp, Marco A. Marra, Maarten van Lohuizen, David B. Lewis, Chad Shaw and Cornelius F. Boerkoel. Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression. (2012) Hum. Mol. Genet. Jun 1; 21(11):2572-87

  9. Danny Leung and Matthew C. Lorincz. Silencing of endogenous retroviruses: when and why do histone marks predominate? (2012) Trends Biochem Sci Volume 37, Issue 4, April, Pages 127–133

  10. Danny Leung, Kevin Dong, Irina A. Maksakova, Preeti Goyal, Ruth Appanah, Sandra Lee, Makoto Tachibana, Yoichi Shinkai, Bernhard Lehnertz, Dixie L. Mager, Fabio M.V. Rossi and Matthew C. Lorincz. Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment but not maintenance of proviral silencing. (2011) PNAS 1014660108v1-201014660.

  11. Mohammad Karimi, Preeti Goyal, Irina A. Maksakova, Misha Bilenky, Danny Leung, Jie Xin Tang, Yoichi Shinkai, Dixie L. Mager, Martin Hirst, Steve Jones and Matthew C. Lorincz DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements and chimaeric transcripts in mouse ES cells. (2011) Cell Stem Cell 8, 676–687

  12. Toshiyuki Matsui*, Danny Leung*, Hiroki Miyashita, Hitoshi Miyachi, Hiroshi Kimura, Makoto Tachibana, Matthew C. Lorincz, Yoichi Shinkai. (2010) Proviral silencing in embryonic stem cells require the histone methyltransferase ESET. Nature 464, 927-931 *-authors contributed equally

  13. Kevin B Dong, Irina A Maksakova, Fabio Mohn, Danny Leung, Ruth Appanah, Sandra Lee, Hao W Yang, Lucia L Lam, Dixie L Mager, Dirk Schübeler, Makoto Tachibana, Yoichi Shinkai, Matthew C Lorincz. DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity. EMBO J. (2008) 27, 2691–2701