Faculty Profiles - LEUNG Danny Chi Yeu | The Hong Kong University of Science and Technology

Danny Chi Yeu LEUNG
梁子宇

PhD in Medical Genetics
The University of British Columbia, 2012

Associate Professor
Division of Life Science

Director of Center for Epigenomics Research

ORCID

0000-0002-2472-894X

Scopus ID

36785209600

Research Interest

Cancer genomics
Epigenomics
Epigenetics
Genome biology
Chromatin structure

Publications

2024 1

Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions

Nature Communications, v. 15, January 2024, article number 15
Tam, Phoebe Lut Fei; Cheung, Ming Fung; Chan, Lu Yan; Leung, Chi Yeu
Article

2023 3

Differential second messenger signaling via dopamine neurons bidirectionally regulates memory retention

Proceedings of the National Academy of Sciences of the United States of America, v. 120, (36), September 2023, article number e2304851120
Takakura, Mai; Lam, Yu Hong; Nakagawa, Reiko; Ng, Man Yung; Hu, Xinyue; Bhargava, Priyanshu; Alia, Abdalla Galaa Mohamed; Gu, Yuzhe; Wang, Zigao; Ota, Takeshi; Kimura, Yoko; Morimoto, Nao; Osakada, Fumitaka; Lee, Ah Young; Leung, Chi Yeu; Miyashita, Tomoyuki; Du, Juan; Okuno, Hiroyuki; Hirano, Yukinori
Article

Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal-fetal interface following SARS-CoV-2 infection

Nature Cell Biology, v. 25, (7), July 2023, p. 1047-1060
Gao, Lin; Mathur, Vrinda; Tam, Ka Man; Zhou, Xuemeng; Cheung, Ming Fung; Chan, Lu Yan; Estrada-Gutierrez, Guadalupe; Leung, Bo Wah; Moungmaithong, Sakita; Wang, Chi Chiu; Poon, Liona C.; Leung, Chi Yeu
Article

The Molecular Impacts of Retrotransposons in Development and Diseases

International Journal of Molecular Sciences, v. 24, (22), November 2023, article number 16418
Tam, Phoebe Lut Fei; Leung, Chi Yeu
Article

2022 1

Implications of the first complete human genome assembly

Genome Research, v. 32, (4), April 2022, p. 595-598
Alkan, Can; Carbone, Lucia; Dennis, Megan; Ernst, Jason; Evrony, Gilad; Girirajan, Santhosh; Leung, Chi Yeu; Cheng, Cheuk Yin; MacAlpine, David; Ni, Ting; Ramsay, Michèle; Rowe, Helen; Gould, Poppy; Enriquez-Gasca, Rocio; Sullivan, Beth
Article

2021 6

DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response

Journal of Neuroscience, v. 41, (45), 10 November 2021, p. 9286-9307
Song, Xuan; Aw, Jacqueline Theeng Mei; Ma, Fulin; Cheung, Ming Fung; Leung, Danny Chi Yeu; Herrup, Karl
Article

Epigenomic and transcriptomic analysis of chronic inflammatory diseases

Genes & Genomics, v. 43, (3), March 2021, article number 12, p. 227-236
Tam, Ka Man; Leung, Chi Yeu Danny
Article

Humanizing the yeast origin recognition complex

Nature Communications, v. 12, (1), January 2021, article number 33
Lee, Clara S.K.; Cheung, Ming Fung; Li, Jinsen; Zhao, Yongqian; Lam, Wai Hei; Ho, Vincy Wing Sze; Rohs, Remo; Zhai, Yuanliang; Leung, Danny; Tye, Bik Kwoon
Article

Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations

Nature Communications, v. 12, (1), 9 November 2021, article number 6462
Zhou, Xuemeng; Sam, Tsz Wing; Lee, Ah Young; Leung, Danny Chi Yeu
Article

Replication timing maintains the global epigenetic state in human cells

Science, v. 372, (6540), April 2021, p. 371-378
Klein, Kyle N.; Zhao, Peiyao A.; Lyu, Xiaowen; Sasaki, Takayo; Bartlett, Daniel A,; Singh, Amar M.; Tasan, Ipek; Zhang, Meng; Watts, Lotte P.; Hiraga, Shin-ichiro; Natsume, Toyoaki; Zhou, Xuemeng; Baslan, Timour; Leung, Chi Yeu; Kanemaki, Masato T.; Donaldson, Anne D.; Zhao, Huimin; Dalton, Stephen; Corces, Victor G.; Gilbert, David M.
Article

Cell-type differential targeting of Setdb1 regulates chromatin looping and cis-regulatory interactions

Leung, Danny Chi Yeu
Conference paper

2020 2

A unified framework for integrative study of heterogeneous gene regulatory mechanisms

Nature Machine Intelligence, v. 2, (8), August 2020, p. 447-456
Cao, Qin; Zhang, Zhenghao; Fu, Alexander Xi; Wu, Qiong; Lee, Tin-Lap; Lo, Eric; Cheng, Alfred S.L.; Cheng, Chao; Leung, Danny Chi Yeu; Yip, Kevin Y.
Article

G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping

Cell Reports, v. 33, (4), 27 October 2020, article number 108315
Jiang, Qinghong; Ang, Ying Jin Julie; Lee, Ah Young; Cao, Qin; Li, Kelly Y.; Yip, Kevin Y.; Leung, Chi Yeu
Article

2018 1

Targeting Epigenetic Modifiers for Cancer Treatments

Current Pharmacology Reports, 5 March 2018, p. 1-9
Leung, Danny Chi Yeu; Chee, chin soon
Article

2016 1

Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development

Molecular Cell, v. 64, (6), December 2016, p. 1062-1073
Zhang, Wenhao; Xia, Weikun; Wang, Qiujun; Towers, Aaron J.; Chen, Jiayu; Gao, Rui; Zhang, Yu; Yen, Chia-An; Lee, Ah Young; Li, Yuanyuan; Zhou, Chen; Liu, Kaili; Zhang, Jing; Gu, Tian-Peng; Chen, Xiuqi; Chang, Zai; Leung, Danny Chi Yeu; Gao, Shaorong; Jiang, Yong-Hui; Xie, Wei
Article

2015 4

Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation

Nature, v. 523, (7559), July 2015, p. 212-216
Schultz, Matthew D.; He, Yupeng; Whitaker, John W.; Hariharan, Manoj; Mukamel, Eran A.; Leung, Danny Chi Yeu; Rajagopal, Nisha; Nery, Joseph R.; Urich, Mark A.; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D.; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J.; Wang, Wei; Ecker, Joseph R.
Article

Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST

Genome Biology, v. 16, (1), October 2015, article number 208
Kelsey, Angela D.; Yang, Christine; Leung, Danny Chi Yeu; Minks, Jakub; Dixon-McDougall, Thomas; Baldry, Sarah El L.; Bogutz, Aaron B.; Lefebvre, Louis; Brown, Carolyn Janet
Article

Integrative analysis of 111 reference human epigenomes

Nature, v. 518, (7539), February 2015, p. 319-329
Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R. David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J.; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K.; Hansen, R. Scott; Kaul, Rajinder; Sabo, Peter J.; Bansal, Mukul S.; Carles, Annaick; Dixon, Jesse R.; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R.; Neph, Shane J.; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C.; Siebenthall, Kyle T.; Sinnott-Armstrong, Nicholas A.; Stevens, Michael; Thurman, Robert E.; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E.; Boyer, Laurie A.; De Jager, Philip L.; Farnham, Peggy J.; Fisher, Susan J.; Haussler, David; Jones, Steven J.M.; Li, Wei; Marra, Marco A.; McManus, Michael T.; Sunyaev, Shamil; Thomson, James A.; Tlsty, Thea D.; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A.; Zhang, Michael Q.; Chadwick, Lisa H.; Bernstein, Bradley E.; Costello, Joseph F.; Ecker, Joseph R.; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A.; Wang, Ting; Kellis, Manolis
Article

Integrative analysis of haplotype-resolved epigenomes across human tissues

Nature, v. 518, (7539), February 2015, p. 350-354
Leung, Danny; Jung, Inkyung; Rajagopal, Nisha; Schmitt, Anthony; Selvaraj, Siddarth; Lee, Ah Young; Yen, Chia-An; Lin, Shin; Lin, Yiing; Qiu, Yunjiang; Xie, Wei; Yue, Feng; Hariharan, Manoj; Ray, Pradipta; Kuan, Samantha; Edsall, Lee; Yang, Hongbo; Chi, Neil C.; Zhang, Michael Q.; Ecker, Joseph R.; Ren, Bing
Article

2014 2

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1

Proceedings of the National Academy of Sciences of the United States of America, v. 111, (18), May 2014, p. 6690-6695
Leung, Danny; Du, Tingting; Wagner, Ulrich; Xie, Wei; Lee, Ah Young; Goyal, Preeti; Li, Yujing; Szulwach, Keith E.; Jin, Peng; Lorincz, Matthew C.; Ren, Bing
Article

The 3D genome in transcriptional regulation and pluripotency

Cell Stem Cell, v. 14, (6), June 2014, p. 771-775
Gorkin, David U.; Leung, Danny; Ren, Bing
Article

2013 1

Epigenomic analysis of multilineage differentiation of human embryonic stem cells

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

2012 2

Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression

Human Molecular Genetics, v. 21, (11), 2012, June, Article number dds083, p. 2572-2587
Baradaran-Heravi, Alireza; Cho, Kyoung Sang; Tolhuis, Bas; Sanyal, Mrinmoy; Morozova, Olena; Morimoto, Marie; Elizondo, Leah I.; Bridgewater, Darren; Lubieniecka, Joanna; Beirnes, Kimberly; Myung, Clara; Leung, Danny; Fam, Hok Khim; Choi, Kunho; Huang, Yan; Dionis, Kira Y.; Zonana, Jonathan; Keller, Kory; Stenzel, Peter; Mayfield, Christy; Luecke, Thomas; Bokenkamp, Arend; Marra, Marco A.; van Lohuizen, Maarten; Lewis, David B.; Shaw, Chad; Boerkoel, Cornelius F.
Article

Silencing of endogenous retroviruses: When and why do histone marks predominate?

Trends in Biochemical Sciences, v. 37, (4), 2012, April, p. 127-133
Leung, Danny; Lorincz, Matthew
Article

2011 2

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mescs

Cell Stem Cell, v.8, (6), 2011, June, p. 676-687
Karimi, Mohammad M.; Goyal, Preeti; Maksakova, Irina A.; Bilenky, Misha; Leung, Danny; Tang, Jie Xin; Shinkai, Yoichi; Mager, Dixie L.; Jones, Steven; Hirst, Martin; Lorincz, Matthew C.
Article

Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing

Proceedings of the National Academy of Sciences of the United States of America, v. 108, (14), 2011, April, p. 5718-5723
Leung, Danny; Dong, Kevin B.; Maksakova, I.A.; Goyal, P.; Appanah, R.; Lee, S.; Tachibana, M.; Shinkai, Y.; Lehnertz, B.; Mager, D.L.; Rossi, F.; Lorincz, M.C.
Article

2010 1

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

Nature, v. 464, (7290), 2010, April, p. 927-931
Matsui, Toshiyuki; Leung, Danny; Miyashita, Hiroki; Maksakova, Irina A.; Miyachi, Hitoshi; Kimura, Hiroshi; Tachibana, Makoto; Lorincz, Matthew C.; Shinkai, Yoichi
Article

2008 1

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity

EMBO Journal, v. 27, (20), 2008, Oct, p. 2691-2701
Dong, K.B.; Maksakova, I.A.; Mohn, F.; Leung, Danny; Appanah, R.; Lee, S.; Yang, H.W.; Lam, L.L.; Mager, D.L.; Schübeler, D.; Tachibana, M.; Shinkai, Y.; Lorincz, M.C.
Article

Article 1

Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions

Nature Communications, v. 15, January 2024, article number 15
Tam, Phoebe Lut Fei; Cheung, Ming Fung; Chan, Lu Yan; Leung, Chi Yeu

Article 3

Differential second messenger signaling via dopamine neurons bidirectionally regulates memory retention

Proceedings of the National Academy of Sciences of the United States of America, v. 120, (36), September 2023, article number e2304851120
Takakura, Mai; Lam, Yu Hong; Nakagawa, Reiko; Ng, Man Yung; Hu, Xinyue; Bhargava, Priyanshu; Alia, Abdalla Galaa Mohamed; Gu, Yuzhe; Wang, Zigao; Ota, Takeshi; Kimura, Yoko; Morimoto, Nao; Osakada, Fumitaka; Lee, Ah Young; Leung, Chi Yeu; Miyashita, Tomoyuki; Du, Juan; Okuno, Hiroyuki; Hirano, Yukinori

Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal-fetal interface following SARS-CoV-2 infection

Nature Cell Biology, v. 25, (7), July 2023, p. 1047-1060
Gao, Lin; Mathur, Vrinda; Tam, Ka Man; Zhou, Xuemeng; Cheung, Ming Fung; Chan, Lu Yan; Estrada-Gutierrez, Guadalupe; Leung, Bo Wah; Moungmaithong, Sakita; Wang, Chi Chiu; Poon, Liona C.; Leung, Chi Yeu

The Molecular Impacts of Retrotransposons in Development and Diseases

International Journal of Molecular Sciences, v. 24, (22), November 2023, article number 16418
Tam, Phoebe Lut Fei; Leung, Chi Yeu

Article 1

Implications of the first complete human genome assembly

Genome Research, v. 32, (4), April 2022, p. 595-598
Alkan, Can; Carbone, Lucia; Dennis, Megan; Ernst, Jason; Evrony, Gilad; Girirajan, Santhosh; Leung, Chi Yeu; Cheng, Cheuk Yin; MacAlpine, David; Ni, Ting; Ramsay, Michèle; Rowe, Helen; Gould, Poppy; Enriquez-Gasca, Rocio; Sullivan, Beth

Article 5

DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response

Journal of Neuroscience, v. 41, (45), 10 November 2021, p. 9286-9307
Song, Xuan; Aw, Jacqueline Theeng Mei; Ma, Fulin; Cheung, Ming Fung; Leung, Danny Chi Yeu; Herrup, Karl

Epigenomic and transcriptomic analysis of chronic inflammatory diseases

Genes & Genomics, v. 43, (3), March 2021, article number 12, p. 227-236
Tam, Ka Man; Leung, Chi Yeu Danny

Humanizing the yeast origin recognition complex

Nature Communications, v. 12, (1), January 2021, article number 33
Lee, Clara S.K.; Cheung, Ming Fung; Li, Jinsen; Zhao, Yongqian; Lam, Wai Hei; Ho, Vincy Wing Sze; Rohs, Remo; Zhai, Yuanliang; Leung, Danny; Tye, Bik Kwoon

Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations

Nature Communications, v. 12, (1), 9 November 2021, article number 6462
Zhou, Xuemeng; Sam, Tsz Wing; Lee, Ah Young; Leung, Danny Chi Yeu

Replication timing maintains the global epigenetic state in human cells

Science, v. 372, (6540), April 2021, p. 371-378
Klein, Kyle N.; Zhao, Peiyao A.; Lyu, Xiaowen; Sasaki, Takayo; Bartlett, Daniel A,; Singh, Amar M.; Tasan, Ipek; Zhang, Meng; Watts, Lotte P.; Hiraga, Shin-ichiro; Natsume, Toyoaki; Zhou, Xuemeng; Baslan, Timour; Leung, Chi Yeu; Kanemaki, Masato T.; Donaldson, Anne D.; Zhao, Huimin; Dalton, Stephen; Corces, Victor G.; Gilbert, David M.

Conference paper 1

Cell-type differential targeting of Setdb1 regulates chromatin looping and cis-regulatory interactions

Leung, Danny Chi Yeu

Article 2

A unified framework for integrative study of heterogeneous gene regulatory mechanisms

Nature Machine Intelligence, v. 2, (8), August 2020, p. 447-456
Cao, Qin; Zhang, Zhenghao; Fu, Alexander Xi; Wu, Qiong; Lee, Tin-Lap; Lo, Eric; Cheng, Alfred S.L.; Cheng, Chao; Leung, Danny Chi Yeu; Yip, Kevin Y.

G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping

Cell Reports, v. 33, (4), 27 October 2020, article number 108315
Jiang, Qinghong; Ang, Ying Jin Julie; Lee, Ah Young; Cao, Qin; Li, Kelly Y.; Yip, Kevin Y.; Leung, Chi Yeu

Article 1

Targeting Epigenetic Modifiers for Cancer Treatments

Current Pharmacology Reports, 5 March 2018, p. 1-9
Leung, Danny Chi Yeu; Chee, chin soon

Article 1

Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development

Molecular Cell, v. 64, (6), December 2016, p. 1062-1073
Zhang, Wenhao; Xia, Weikun; Wang, Qiujun; Towers, Aaron J.; Chen, Jiayu; Gao, Rui; Zhang, Yu; Yen, Chia-An; Lee, Ah Young; Li, Yuanyuan; Zhou, Chen; Liu, Kaili; Zhang, Jing; Gu, Tian-Peng; Chen, Xiuqi; Chang, Zai; Leung, Danny Chi Yeu; Gao, Shaorong; Jiang, Yong-Hui; Xie, Wei

Article 4

Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation

Nature, v. 523, (7559), July 2015, p. 212-216
Schultz, Matthew D.; He, Yupeng; Whitaker, John W.; Hariharan, Manoj; Mukamel, Eran A.; Leung, Danny Chi Yeu; Rajagopal, Nisha; Nery, Joseph R.; Urich, Mark A.; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D.; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J.; Wang, Wei; Ecker, Joseph R.

Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST

Genome Biology, v. 16, (1), October 2015, article number 208
Kelsey, Angela D.; Yang, Christine; Leung, Danny Chi Yeu; Minks, Jakub; Dixon-McDougall, Thomas; Baldry, Sarah El L.; Bogutz, Aaron B.; Lefebvre, Louis; Brown, Carolyn Janet

Integrative analysis of 111 reference human epigenomes

Nature, v. 518, (7539), February 2015, p. 319-329
Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R. David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J.; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K.; Hansen, R. Scott; Kaul, Rajinder; Sabo, Peter J.; Bansal, Mukul S.; Carles, Annaick; Dixon, Jesse R.; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R.; Neph, Shane J.; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C.; Siebenthall, Kyle T.; Sinnott-Armstrong, Nicholas A.; Stevens, Michael; Thurman, Robert E.; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E.; Boyer, Laurie A.; De Jager, Philip L.; Farnham, Peggy J.; Fisher, Susan J.; Haussler, David; Jones, Steven J.M.; Li, Wei; Marra, Marco A.; McManus, Michael T.; Sunyaev, Shamil; Thomson, James A.; Tlsty, Thea D.; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A.; Zhang, Michael Q.; Chadwick, Lisa H.; Bernstein, Bradley E.; Costello, Joseph F.; Ecker, Joseph R.; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A.; Wang, Ting; Kellis, Manolis

Integrative analysis of haplotype-resolved epigenomes across human tissues

Nature, v. 518, (7539), February 2015, p. 350-354
Leung, Danny; Jung, Inkyung; Rajagopal, Nisha; Schmitt, Anthony; Selvaraj, Siddarth; Lee, Ah Young; Yen, Chia-An; Lin, Shin; Lin, Yiing; Qiu, Yunjiang; Xie, Wei; Yue, Feng; Hariharan, Manoj; Ray, Pradipta; Kuan, Samantha; Edsall, Lee; Yang, Hongbo; Chi, Neil C.; Zhang, Michael Q.; Ecker, Joseph R.; Ren, Bing

Article 2

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1

Proceedings of the National Academy of Sciences of the United States of America, v. 111, (18), May 2014, p. 6690-6695
Leung, Danny; Du, Tingting; Wagner, Ulrich; Xie, Wei; Lee, Ah Young; Goyal, Preeti; Li, Yujing; Szulwach, Keith E.; Jin, Peng; Lorincz, Matthew C.; Ren, Bing

The 3D genome in transcriptional regulation and pluripotency

Cell Stem Cell, v. 14, (6), June 2014, p. 771-775
Gorkin, David U.; Leung, Danny; Ren, Bing

Article 1

Epigenomic analysis of multilineage differentiation of human embryonic stem cells

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

Article 2

Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression

Human Molecular Genetics, v. 21, (11), 2012, June, Article number dds083, p. 2572-2587
Baradaran-Heravi, Alireza; Cho, Kyoung Sang; Tolhuis, Bas; Sanyal, Mrinmoy; Morozova, Olena; Morimoto, Marie; Elizondo, Leah I.; Bridgewater, Darren; Lubieniecka, Joanna; Beirnes, Kimberly; Myung, Clara; Leung, Danny; Fam, Hok Khim; Choi, Kunho; Huang, Yan; Dionis, Kira Y.; Zonana, Jonathan; Keller, Kory; Stenzel, Peter; Mayfield, Christy; Luecke, Thomas; Bokenkamp, Arend; Marra, Marco A.; van Lohuizen, Maarten; Lewis, David B.; Shaw, Chad; Boerkoel, Cornelius F.

Silencing of endogenous retroviruses: When and why do histone marks predominate?

Trends in Biochemical Sciences, v. 37, (4), 2012, April, p. 127-133
Leung, Danny; Lorincz, Matthew

Article 2

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mescs

Cell Stem Cell, v.8, (6), 2011, June, p. 676-687
Karimi, Mohammad M.; Goyal, Preeti; Maksakova, Irina A.; Bilenky, Misha; Leung, Danny; Tang, Jie Xin; Shinkai, Yoichi; Mager, Dixie L.; Jones, Steven; Hirst, Martin; Lorincz, Matthew C.

Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing

Proceedings of the National Academy of Sciences of the United States of America, v. 108, (14), 2011, April, p. 5718-5723
Leung, Danny; Dong, Kevin B.; Maksakova, I.A.; Goyal, P.; Appanah, R.; Lee, S.; Tachibana, M.; Shinkai, Y.; Lehnertz, B.; Mager, D.L.; Rossi, F.; Lorincz, M.C.

Article 1

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

Nature, v. 464, (7290), 2010, April, p. 927-931
Matsui, Toshiyuki; Leung, Danny; Miyashita, Hiroki; Maksakova, Irina A.; Miyachi, Hitoshi; Kimura, Hiroshi; Tachibana, Makoto; Lorincz, Matthew C.; Shinkai, Yoichi

Article 1

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity

EMBO Journal, v. 27, (20), 2008, Oct, p. 2691-2701
Dong, K.B.; Maksakova, I.A.; Mohn, F.; Leung, Danny; Appanah, R.; Lee, S.; Yang, H.W.; Lam, L.L.; Mager, D.L.; Schübeler, D.; Tachibana, M.; Shinkai, Y.; Lorincz, M.C.

2018 1

Targeting Epigenetic Modifiers for Cancer Treatments

Current Pharmacology Reports, 5 March 2018, p. 1-9
Leung, Danny Chi Yeu; Chee, chin soon
Article

2016 1

Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development

Molecular Cell, v. 64, (6), December 2016, p. 1062-1073
Zhang, Wenhao; Xia, Weikun; Wang, Qiujun; Towers, Aaron J.; Chen, Jiayu; Gao, Rui; Zhang, Yu; Yen, Chia-An; Lee, Ah Young; Li, Yuanyuan; Zhou, Chen; Liu, Kaili; Zhang, Jing; Gu, Tian-Peng; Chen, Xiuqi; Chang, Zai; Leung, Danny Chi Yeu; Gao, Shaorong; Jiang, Yong-Hui; Xie, Wei
Article

2015 4

Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation

Nature, v. 523, (7559), July 2015, p. 212-216
Schultz, Matthew D.; He, Yupeng; Whitaker, John W.; Hariharan, Manoj; Mukamel, Eran A.; Leung, Danny Chi Yeu; Rajagopal, Nisha; Nery, Joseph R.; Urich, Mark A.; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D.; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J.; Wang, Wei; Ecker, Joseph R.
Article

Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST

Genome Biology, v. 16, (1), October 2015, article number 208
Kelsey, Angela D.; Yang, Christine; Leung, Danny Chi Yeu; Minks, Jakub; Dixon-McDougall, Thomas; Baldry, Sarah El L.; Bogutz, Aaron B.; Lefebvre, Louis; Brown, Carolyn Janet
Article

Integrative analysis of 111 reference human epigenomes

Nature, v. 518, (7539), February 2015, p. 319-329
Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R. David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J.; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K.; Hansen, R. Scott; Kaul, Rajinder; Sabo, Peter J.; Bansal, Mukul S.; Carles, Annaick; Dixon, Jesse R.; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R.; Neph, Shane J.; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C.; Siebenthall, Kyle T.; Sinnott-Armstrong, Nicholas A.; Stevens, Michael; Thurman, Robert E.; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E.; Boyer, Laurie A.; De Jager, Philip L.; Farnham, Peggy J.; Fisher, Susan J.; Haussler, David; Jones, Steven J.M.; Li, Wei; Marra, Marco A.; McManus, Michael T.; Sunyaev, Shamil; Thomson, James A.; Tlsty, Thea D.; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A.; Zhang, Michael Q.; Chadwick, Lisa H.; Bernstein, Bradley E.; Costello, Joseph F.; Ecker, Joseph R.; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A.; Wang, Ting; Kellis, Manolis
Article

Integrative analysis of haplotype-resolved epigenomes across human tissues

Nature, v. 518, (7539), February 2015, p. 350-354
Leung, Danny; Jung, Inkyung; Rajagopal, Nisha; Schmitt, Anthony; Selvaraj, Siddarth; Lee, Ah Young; Yen, Chia-An; Lin, Shin; Lin, Yiing; Qiu, Yunjiang; Xie, Wei; Yue, Feng; Hariharan, Manoj; Ray, Pradipta; Kuan, Samantha; Edsall, Lee; Yang, Hongbo; Chi, Neil C.; Zhang, Michael Q.; Ecker, Joseph R.; Ren, Bing
Article

2014 2

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1

Proceedings of the National Academy of Sciences of the United States of America, v. 111, (18), May 2014, p. 6690-6695
Leung, Danny; Du, Tingting; Wagner, Ulrich; Xie, Wei; Lee, Ah Young; Goyal, Preeti; Li, Yujing; Szulwach, Keith E.; Jin, Peng; Lorincz, Matthew C.; Ren, Bing
Article

The 3D genome in transcriptional regulation and pluripotency

Cell Stem Cell, v. 14, (6), June 2014, p. 771-775
Gorkin, David U.; Leung, Danny; Ren, Bing
Article

2013 1

Epigenomic analysis of multilineage differentiation of human embryonic stem cells

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

2012 2

Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression

Human Molecular Genetics, v. 21, (11), 2012, June, Article number dds083, p. 2572-2587
Baradaran-Heravi, Alireza; Cho, Kyoung Sang; Tolhuis, Bas; Sanyal, Mrinmoy; Morozova, Olena; Morimoto, Marie; Elizondo, Leah I.; Bridgewater, Darren; Lubieniecka, Joanna; Beirnes, Kimberly; Myung, Clara; Leung, Danny; Fam, Hok Khim; Choi, Kunho; Huang, Yan; Dionis, Kira Y.; Zonana, Jonathan; Keller, Kory; Stenzel, Peter; Mayfield, Christy; Luecke, Thomas; Bokenkamp, Arend; Marra, Marco A.; van Lohuizen, Maarten; Lewis, David B.; Shaw, Chad; Boerkoel, Cornelius F.
Article

Silencing of endogenous retroviruses: When and why do histone marks predominate?

Trends in Biochemical Sciences, v. 37, (4), 2012, April, p. 127-133
Leung, Danny; Lorincz, Matthew
Article

2011 2

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mescs

Cell Stem Cell, v.8, (6), 2011, June, p. 676-687
Karimi, Mohammad M.; Goyal, Preeti; Maksakova, Irina A.; Bilenky, Misha; Leung, Danny; Tang, Jie Xin; Shinkai, Yoichi; Mager, Dixie L.; Jones, Steven; Hirst, Martin; Lorincz, Matthew C.
Article

Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing

Proceedings of the National Academy of Sciences of the United States of America, v. 108, (14), 2011, April, p. 5718-5723
Leung, Danny; Dong, Kevin B.; Maksakova, I.A.; Goyal, P.; Appanah, R.; Lee, S.; Tachibana, M.; Shinkai, Y.; Lehnertz, B.; Mager, D.L.; Rossi, F.; Lorincz, M.C.
Article

2010 1

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

Nature, v. 464, (7290), 2010, April, p. 927-931
Matsui, Toshiyuki; Leung, Danny; Miyashita, Hiroki; Maksakova, Irina A.; Miyachi, Hitoshi; Kimura, Hiroshi; Tachibana, Makoto; Lorincz, Matthew C.; Shinkai, Yoichi
Article

2008 1

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity

EMBO Journal, v. 27, (20), 2008, Oct, p. 2691-2701
Dong, K.B.; Maksakova, I.A.; Mohn, F.; Leung, Danny; Appanah, R.; Lee, S.; Yang, H.W.; Lam, L.L.; Mager, D.L.; Schübeler, D.; Tachibana, M.; Shinkai, Y.; Lorincz, M.C.
Article

No Publications

Teaching Assignment

LIFS3140

General Genetics

LIFS4981	Biochemistry and Cell Biology Project Research II
LIFS6116G	Current Topics in Genomics and Bioinformatics

LIFS4973	Biotechnology Project Research I
SCIE4500	IRE Research Project II

No Teaching Assignments

Research Postgraduate (RPG) Supervision

From January 2021 to December 2024 (As of 21 November 2024)

Current RPGs

Doctor of Philosophy

KAN, Ying Hei
Life Science
MATHUR, Vrinda
Life Science
JIANG, Qinghong
Life Science
LIU, Kwok Yu
Life Science
WAI, Geena
Life Science
CHENG, Cheuk Yin
Life Science

Master of Philosophy

WANG, Wenxin
Life Science
KANG, Juwon
Life Science
LAM, Tsz Kwan
Life Science

Graduated RPGs

Doctor of Philosophy

GAO, Lin
Life Science( Completed in 2024 )
TAM, Ka Man
Life Science( Completed in 2024 )
TAM, Lut Fei
Life Science( Completed in 2024 )
AW, Jacqueline Theeng Mei
Life Science( Completed in 2023 )
ZHOU, Xuemeng
Life Science( Completed in 2021 )

Master of Philosophy

KAN, Ying Hei
Life Science( Completed in 2023 )
MATHUR, Vrinda
Life Science( Completed in 2022 )
JIANG, Qinghong
Life Science( Completed in 2021 )
LIU, Kwok Yu
Life Science( Completed in 2021 )
WAI, Geena
Life Science( Completed in 2021 )

Projects

From January 2022 to December 2024

Elucidating how retrotransposons impact immune modulation in autoimmune diseases

解析逆轉錄子如何影響自體免疫疾病中的免疫調節 Leading

RGC - General Research Fund
Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)
2024 -
Elucidating the impact of Setdb1 on genome architecture in cellular differentiation and disease

研究 Setdb1 對細胞分化和疾病中基因組結構的影響 Leading

RGC - General Research Fund
Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)
2024 -
Development of Low-input and Single-cell Epigenomic Profiling Method for Co-occurring Chromatin Features

開發用於測量共現染色質特徵的低輸入單細胞表觀基因組分析技術 Leading

Innovation and Technology Fund, New Horizon Health Limited
Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)
2024 -
Stem cell-niche interactions in tissue maintenance and engineering

幹細胞與微環境互作在組織維持和組織工程中的應用 Participating

RGC - Theme-based Research Scheme
Project Team (HKUST)
XIE Ting (Lead)

CHEUNG Tom

GUO Yusong

LEUNG Danny Chi Yeu

LIU Kai

MAK Ho Yi

SUN Fei

WU Angela Ruohao

WU Zhenguo

YAN Yan
2022 -
Characterizing cytoplasmic DNA in neurodegenerative disease mouse models

歸納細胞質 DNA在神經退行性疾病中的特徵 Leading

RGC - General Research Fund
Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)
2022 -
Delineating the role of retrotransposons in placenta development and disease

反轉錄轉座子與胎盤發育和疾病 Leading

RGC - General Research Fund
Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)
2022 -
The Center for Neurodegenerative Diseases

N/A Participating

Innovation and Technology Fund
Project Team (HKUST)
IP Nancy Yuk-Yu (Lead)

CHEUNG Tom

FU Amy Kit Yu

LEUNG Danny Chi Yeu

LIU Kai

WANG Jiguang

WONG Yung Hou

WU Zhenguo
2020 -
Molecular regulation of quiescence and early activation in muscle stem cells

骨骼肌幹細胞靜息態及早期活化的分子調控 Participating

RGC - Collaborative Research Fund
Project Team (HKUST)
WU Zhenguo (Lead)

CHEUNG Tom

LEUNG Danny Chi Yeu
2020 - 2024
Hong Kong Epigenomics Project Leading

Lo Ka Chung Charitable Foundation Limited
Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)
2018 -
Deciphering the epigenome of melanomas Leading

Croucher Foundation
Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)
2017 - 2023

Research Interest

Publications

2024 1

2023 3

2022 1

2021 6

2020 2

2018 1

2016 1

2015 4

2014 2

2013 1

2012 2

2011 2

2010 1

2008 1

Article 1

Article 3

Article 1

Article 5

Conference paper 1

Article 2

Article 1

Article 1

Article 4

Article 2

Article 1

Article 2

Article 2

Article 1

Article 1

2018 1

2016 1

2015 4

2014 2

2013 1

2012 2

2011 2

2010 1

2008 1

Teaching Assignment

Research Postgraduate (RPG) Supervision

From January 2021 to December 2024 (As of 21 November 2024)

Current RPGs

Graduated RPGs

Projects

From January 2022 to December 2024

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