Publications

Publications

* Co-first Authorship # Corresponding Authorship

Selected Publications:

  1. Yi Liu*, Haochen Ni*, Jie Li*, Jing Yang, Ivann Sekielyk, Bryan E. Snow, Zihao Zhang, Feifan Zhang, Michael St. Paul, Jinyi Han, Meghan Kates, Shaofeng Liu, Yawei Zhang, Zurui Huang, Yin Xu, Samuel D. Saibil, Tak W. Mak, Dali Han#, Meng Michelle Xu#; LARP4-mediated hypertranslation drives T cell dysfunction in tumors, Nature Immunology, 2025, published online. [PDF Download]
  2. Guanghao Liang*, Linchen Wang*, Qiancheng You*, Kirk Cahil*, Chuanyuan Chen, Wei Zhang, Noreen Fulton, Wendy Stock, Olatoyosi Odenike#, Chuan He#, Dali Han#. Cellular Composition and 5hmC Signature Predict the Treatment Response of AML Patients to Azacitidine Combined with Chemotherapy. Advanced Science, 2023, 10, 2300445. [PDF Download]
  3. Lihui Dong*, Chuanyuan Chen*, Yawei Zhang*, Peijin Guo, Zhenghang Wang, Jian Li, Yi Liu, Jun Liu, Renbao Chang, Yilin Li, Guanghao Liang, Weiyi Lai, Mengxue Sun, Urszula Dougherty, Marc B. Bissonnette, Hailin Wang, Lin Shen, Meng Michelle Xu#, Dali Han#. The loss of RNA N6-adenosine methyltransferase Mettl14 in tumor-associated macrophages promotes CD8+ T cell dysfunction and tumor growth. Cancer Cell, 2021, 33, 1221-1233. [PDF Download]
  4. Yi Liu*, Guanghao Liang*, Hongjiao Xu*, Wenxin Dong*, Ze Dong*, Zhiwei Qiu, Zihao Zhang, Fangle Li, Yue Huang, Yilin Li, Jun Wu, Shenyi Yin, Yawei Zhang, Peijin Guo, Jun Liu, Jianzhong Jeff Xi, PengJiang, Dali Han#, Caiguang Yang#, Meng Michelle Xu#. Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance. Cell Metabolism, 2021, 33, 1221-1233. e11. [PDF Download]
  5. Jun Liu*, Xiaoyang Dou*, Chuanyuan Chen*, Chuan Chen, Chang Liu, Meng Michelle Xu, Siqi Zhao, Bin Shen, Yawei Gao#, Dali Han#, Chuan He#. N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription. Science, 2020, 367, 580-586. [PDF Download]
  6. Dali Han*#, Jun Liu*, Chuanyuan Chen, Lihui Dong, Yi Liu, Renbao Chang, Xiaona Huang, Yuanyuan Liu, Jianying Wang, Urszula Dougherty, Marc B Bissonnette, Bin Shen, Ralph R Weichselbaum, Meng Michelle Xu#, Chuan He#. Anti-tumour immunity controlled through mRNA m6A methylation and YTHDF1 in dendritic cells. Nature, 2019, 566, 270-274. [PDF Download]
  7. Xin Tian*, Baofa Sun*, Chuanyuan Chen*, Chunchun Gao*, Ji Zhang*, Xingyu Lu*, Linchen Wang, Xiangnan Li, Yurong Xing, Ruijuan Liu, Xiao Han, Zheng Qi, Xiaojian Zhang, Chuan He, Dali Han#, Yun-Gui Yang#, Quancheng Kan#. Circulating tumor DNA 5-hydroxymethylcytosine as a novel diagnostic biomarker for esophageal cancer. Cell research, 2018, 28, 597. [PDF Download]
  8. Dali Han*, Xingyu Lu*, Alan H. Shih*, Ji Nie, Qiancheng You, Meng Michelle Xu, Ari M. Melnick, Ross L. Levine#, Chuan He#. A highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations. Molecular Cell, 2016, 63, 711–719. [PDF Download]

Invited Review:

1.Dali Han, Meng Michelle Xu. RNA Modification in the Immune System. Annual Review of Immunology, 2023, 41, 73-98. [PDF Download]

Other Publications:

  1. Fangle Li*, Feifan Zhang*, Jie Li*, Yu Zhang*, Wenxuan Gong, Yawei Zhang, Mengxia Liu, Jie Ren#, Dali Han#. Dual roles of N6-methyladenosine in R-loop regulation of gene transcription and genome stability. Science China. Life sciences, 2025, published online. [PDF Download]
  2. Tingyue Gong*, Zhiyang Zeng*, Zurui Huang*, Yang Luo*, Xiya Cao, Hao Li, Yongheng Zhao, Dali Han#, Dali Li#, Ming Zhong#. Downregulation of METTL3 enhances TRADD-mediated apoptosis in inflammatory bowel disease. Science China. Life sciences, 2025, 68, 2010-2027. [PDF Download]
  3. Chuandong Liu*, Jie Li*, Hua Jin*, Qian Zhao*, Fangle Li, Zurui Huang, Boyuan Mei, Wenxuan Gong#, Xia Wang#, Dali Han#. Colonic stem cell from severe ulcerative colitis maintains environment-independent immune activation by altering chromatin accessibility and global m6A loss. Life Medicine, 2023, 2,  lnad034.
  4. Guanshen Cui*, Jia-Yi Zhou*, Xin-Yang Ge*, Bao-Fa Sun*, Ge-Ge Song*, Xing Wang*, Xiu-Zhi Wang, Rui Zhang, Hai-Lin Wang, Qing Jing, Magdalena J. Koziol, Yong-Liang Zhao, An Zeng, Wei-Qi Zhang#, Da-Li Han#, Yun-Gui Yang#, Ying Yang#. m6A promotes planarian regeneration, Cell Proliferation, 2023, 56, e13481.
  5. Xiaoyang Jin, Zurui Huang, Lijun Xie, Li Liu, Dali Han#, Liang Cheng#. Photo‐Facilitated Detection and Sequencing of 5‐Formylcytidine RNA. Angewandte Chemie-International Edition, 2022, 61, e202210652.
  6. Chi Xu*, Zunhui Ke*, Chuandong Liu*, Zhihao Wang*, Denghui Liu, Lei Zhang, Jingning Wang, Wenjun He, Zhimeng Xu, Yanqing Li, Yanan Yang, Zhaowei Huang, Panjing Lv, Xin Wang, Dali Han#, Yan Li#, Nan Qiao#, and Bing Liu#. Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server. Journal of Chemical Information and Modeling, 2020, 60, 5735-5745.
  7. Junya Peng*, Bao-Fa Sun*, Chuan-Yuan Chen*, Jia-Yi Zhou*, Yu-Sheng Chen*, Hao Chen, Lulu Liu, Dan Huang, Jialin Jiang, Guan-Shen Cui, Ying Yang, Wenze Wang, Dan Guo, Menghua Dai, Junchao Guo, Taiping Zhang, Quan Liao, Yi Liu, Yong-Liang Zhao, Da-Li Han*, Yupei Zhao#, Yun-Gui Yang#, Wenming Wu#. Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Research, 2019, 29, 725-738.
  8. Tongnian Gu*, Siqi Zhao*, Yishuang Pi, Weizhong Chen, Chuanyuan Chen, Qian Liu, Min Li, Dali Han#, Quanjiang Ji#. Highly efficient base editing in Staphylococcus aureus using an engineered CRISPR RNA-guided cytidine deaminase. Chemical Science, 2018, 9, 3248-3253.
  9. Qing Dai*, Sharon Moshitch-Moshkovitz*, Dali Han*, Nitzan Kol, Ninette Amariglio, Gideon Rechavi, Dan Dominissini, Chuan He. Nm-seq maps 2′-O-methylation sites in human mRNA with base precision. Nature Methods, 2017, 14, 695.
  10. Bo Xia*, Dali Han*, Xingyu Lu*, Zhaozhu Sun, Ankun Zhou, Qiangzong Yin, Hu Zeng, Menghao Liu, Xiang Jiang, Wei Xie, Chuan He, Chengqi Yi. Bisulfite-free, Base-resolution analysis of 5-formylcytosine at the genome scale. Nature Methods, 2015, 12, 1047-1050.
  11. Meng Michelle Xu*, Yang Pu, Dali Han, Yaoyao Shi, Xuezhi Cao, Hua Liang, Xiang Chen, Xiao-Dong Li, Liufu Deng, Zhijian J. Chen, Ralph R. Weichselbaum, and Yang-Xin Fu#. Dendritic cells but not macrophages sense tumor mitochondrial DNA for cross-priming through signal regulatory protein α signaling. Immunity, 2017, 47, 363–373. e5.
  12. Dan Dominissini*#, Sigrid Nachtergaele*, Sharon Moshitch-Moshkovitz*, Eyal Peer, Nitzan Kol, Moshe Shay Ben-Haim, Qing Dai, Ayelet Di Segni, Mali Salmon-Divon, Wesley C. Clark, Guanqun Zheng, Tao Pan, Oz Solomon, Eran Eyal, Vera Hershkovitz, Dali Han, Louis C. Doré, Ninette Amariglio, Gideon Rechavi#, Chuan He#. The dynamic N-1-methyladenosine methylome in eukaryotic messenger RNA. Nature, 2016, 530, 441-446.
  13. Fange Liu*, Wesley Clark, Guanzheng Luo, Xiaoyun Wang, Ye Fu, Jiangbo Wei, Xiao Wang, Ziyang Hao, Qing Dai, Guanqun Zheng, Honghui Ma, Dali Han, Molly Evans, Arne Klungland, Tao Pan#, and Chuan He#. ALKBH1-mediated tRNA demethylation regulates translation. Cell, 2016, 167(3): 816-828.e16.
  14. Jianzhao Liu*, Yuanxiang Zhu*, Guan-Zheng Luo*, Xinxia Wang*, Yanan Yue, Xiaona Wang, Xin Zong, Kai Chen, Hang Yin, Ye Fu, Dali Han, Yizhen Wang#, Dahua Chen#, & Chuan He#. Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig. Nature communications, 2016, 7, 13052.
  15. Qing Dai*, Paul J. Sanstead*, Chunte Sam Peng*, Dali Han, Chuan He#, and Andrei Tokmakoff#. Weakened N3 hydrogen bonding by 5-formylcytosine and 5-carboxylcytosine reduces their base-pairing stability. ACS chemical biology, 2016, 11, 470-477.
  16. Xingyu Lu*, Dali Han*, Zhao Boxuan Simen*, ChunXiao Song, LiSheng Zhang, Louis C Doré, Chuan He#. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Research, 2015, 25, 386-389.
  17. Xiao Wang*, Boxuan Simen Zhao*, Ian A Roundtree, Zhike Lu, Dali Han, Honghui Ma, Xiaocheng Weng, Kai Chen, Hailing Shi, Chuan He#. N-6-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell, 2015, 161, 1388-1399.
  18. Ye Fu*, Guanzheng Luo*, Kai Chen, Xin Deng, Miao Yu, Dali Han, Ziyang Hao, Jianzhao Liu, Xingyu Lu, Louis C Doré, Xiaocheng Weng, Quanjiang Ji, Laurens Mets, Chuan He#. N-6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas. Cell, 2015, 161, 879-892.
  19. Jing Wang*, Cheng Luo*, Changliang Shan*, Qiancheng You*, Junyan Lu, Shannon Elf, Yu Zhou, Yi Wen, Jan L. Vinkenborg, Jun Fan, Heebum Kang, Ruiting Lin, Dali Han, Yuxin Xie, Jason Karpus, Shijie Chen, Shisheng Ouyang, Chihao Luan, Naixia Zhang, Hong Ding, Maarten Merkx, Hong Liu, Jing Chen#, Hualiang Jiang#, Chuan He#. Inhibition of human copper trafficking by a small molecule significantly attenuates cancer cell proliferation. Nature Chemistry, 2015, 7, 968-979.
  20. Kai Chen*, Zhike Lu*, Xiao Wang, Ye Fu, GuanZheng Luo, Nian Liu, Dali Han, Dan Dominissini, Qing Dai, Tao Pan, Chuan He#. High-Resolution N-6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing. Angewandte Chemie International Edition in English, 2015, 54, 1587-1590.
  21. Ming Su*, Dali Han*, Jerome BoydKirkup, Xiaoming Yu, JingDong J Han#. Evolution of Alu Elements toward Enhancers. Cell Reports, 2014, 7, 376-385.
  22. Jianzhao Liu*, Yanan Yue*, Dali Han, Xiao Wang, Ye Fu, Liang Zhang, Guifang Jia, Miao Yu, Zhike Lu, Xin Deng, Qing Dai, Weizhong Chen, Chuan He#. A METTL3-METTL14 complex mediates mammalian nuclear RNA N-6-adenosine methylation. Nature Chemical Biology, 2014, 10, 93-95.
  23. Xiao Wang, Zhike Lu, Adrian Gomez, Gary C Hon, Yanan Yue, Dali Han, Ye Fu, Marc Parisien, Qing Dai, Guifang Jia, Bing Ren, Tao Pan, Chuan He#. N-6-methyladenosine-dependent regulation of messenger RNA stability. Nature, 2014, 505, 117-120.
  24. Yixing Han*, Dali Han*, Zheng Yan, Jerome D BoydKirkup, Christopher D Green, Philipp Khaitovich, JingDong J Han#. Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain. Aging cell, 2012, 11, 1055-1064.
  25. Chunyu Jin*, Jing Li*, Christopher D Green, Xiaoming Yu, Xia Tang, Dali Han, Bo Xian, Dan Wang, Xinxin Huang, Xiongwen Cao, Zheng Yan, Lei Hou, Jiancheng Liu, Nicholas Shukeir, Philipp Khaitovich, Charlie D Chen, Hong Zhang, Thomas Jenuwein, JingDong J Han#. Histone Demethylase UTX1-Regulates C. elegans Life Span by Targeting the Insulin/IGF-1 Signaling Pathway. Cell metabolism, 2011, 14, 161-172.
  26. Yi Liu*, Dali Han*, Yixing Han*, Zheng Yan, Bin Xie, Jing Li, Nan Qiao, Haiyang Hu, Philipp Khaitovich, Yuan Gao, JingDong J Han#. Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Research, 2011, 39, 1408-1418.