PUBLICATIONS
Update Date:   2024-03-10

Selected Publications

# Correspondence author

* First author

** Second author

  1. Lijia Li,* Fangnong Lai,* Ling Liu, Xukun Lu, Xiaoyu Hu, Bofeng Liu, Zili Lin, Qiang Fan, Feng Kong, Qianhua Xu,Wei Xie#. Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos. Nat Struct Mol Biol (2024).
  2. Lijia Li,* Fangnong Lai,* Xiaoyu Hu,* Bofeng Liu,* Xukun Lu, Zili Lin, Ling Liu, Yunlong Xiang, Tristan Frum, Michael A. Halbisen, Fengling Chen, Qiang Fan, Amy Ralston, and Wei Xie#. Multifaceted SOX2-chromatin interaction underpins pluripotency progression in early embryos. Science 2023 Dec 15;382(6676):eadi5516 (2023).
  3. Dongdong Qin,* Yayun Gu,* Yu Zhang,* Shu Wang,* Tao Jiang, Yao Wang, Cheng Wang, Chang Chen, Tao Zhang, Weiya Xu, Hanben Wang, Ke Zhang, Liangjun Hu, Lufan Li, Wei Xie,# Xin Wu,# Zhibin Hu#. Phase-separated CCER1 coordinates the histone-to-protamine transition and male fertility. Nat Commun 2023 Dec 11;14(1):8209 (2023).
  4. Fangnong Lai,* Lijia Li,* Xiaoyu Hu,* Bofeng Liu,* Ziqi Zhu, Ling Liu, Qiang Fan, Huabin Tian, Kai Xu, Xukun Lu, Qing Li, Kong Feng, Lijuan Wang, Zili Lin, Hongyu Deng, Jinsong Li and Wei Xie#. NR5A2 connects zygotic genome activation to the first lineage segregation in totipotent embryos.Cell Res (2023).
  5. Xiaoqing Nie,* Qianhua Xu,* Chengpeng Xu,* Fengling Chen,* Qizhi Wang, Dandan Qin, Rui Wang, Zheng Gao, Xukun Lu, Xinai Yang, Yu Wu, Chen Gu, Wei Xie,# and Lei Li#. Maternal TDP-43 interacts with RNA Pol II and regulates zygotic genome activation. Nat Commun 2023 Jul 17;14(1):4275 (2023).
  6. Shuyan Ji,* Fengling Chen,* Paula Stein,* Jiacheng Wang,* Ziming Zhou,* Lijuan Wang,* Qing Zhao,** Zili Lin,** Bofeng Liu, Kai Xu, Fangnong Lai, Zhuqing Xiong, Xiaoyu Hu, Tianxiang Kong, Feng Kong, Bo Huang, Qiujun Wang, Qianhua Xu, Qiang Fan, Ling Liu, Carmen J. Williams, Richard M. Schultz,# and Wei Xie#. OBOX regulates mouse zygotic genome activation and early development. Nature (2023).
  7. Hongmei Zhang,* Shuyan Ji,* Ke Zhang,* Yuling Chen, Jia Ming, Feng Kong, Lijun Wang, Shun Wang, Zhuoning Zou, Zhuqing Xiong, Kai Xu, Zili Lin, Bo Huang, Ling Liu, Qiang Fan, Suoqin Jin, Haiteng Deng,# and Wei Xie #. Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition. Genome Biol 2023 Jul 13;24(1):166 (2023).
  8. Xiaotong Wu,* Xi Wu, Wei Xie #. Activation, decommissioning, and dememorization: enhancers in a life cycle. Trends in Biochemical Sciences ISSN 0968-0004 (2023).
  9. Zhuoning Zou,* Chuanxin Zhang,* Qiuyan Wang,* Zhenzhen Hou,* Zhuqing Xiong, Feng Kong, Qiujun Wang, Jinzhu Song, Boyang Liu, Bofeng Liu, Lijuan Wang, Fangnong Lai, Qiang Fan, Wenrong Tao, Shuai Zhao, Xiaonan Ma, Miao Li, Keliang Wu, Han Zhao,# Zijiang Chen,# and Wei Xie #. Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation. Science 2022 Sep 8:eabo7923 (2022).
  10. Zhuqing Xiong,* Kai Xu,* Zili Lin,* Feng Kong,* Qiujun Wang,* Yujun Quan, Qian-qian Sha, Fajin Li, Zhuoning Zou, Ling Liu, Shuyan Ji, Yuling Chen, Hongmei Zhang, Jianhuo Fang, Guang Yu, Bofeng Liu, Lijuan Wang, Huili Wang, Haiteng Deng, Xuerui Yang, Heng-yu Fan, Lei Li,# and Wei Xie #. Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development. Nat Cell Biol 24, 968–980 (2022).
  11. Yu Zhang,* Wei Xie#. Building the genome architecture during the maternal to zygotic transition. Curr Opin Genet Dev. 2022 Feb;72:91-100. (2022).
  12. Xiaotong Wu,* Hongmei Zhang,* Bingjie Zhang,* Yu Zhang, Qiuyan Wang, Weimin Shen, Xi Wu, Lijia Li, Weikun Xia, Ryohei Nakamura, Bofeng Liu, Feng Liu, Hiroyuki Takeda, Anming Meng, Wei Xie#.Methylome inheritance and enhancer dememorization reset an epigenetic gate safeguarding embryonic programs.Science Advances. 2021;7(52):eabl3858. doi:10.1126/sciadv.abl3858 (2021).
  13. Xukun Lu,* Yu Zhang,* Lijuan Wang,* Leyun Wang,* Huili Wang, Qianhua Xu, Yunlong Xiang, Chaolei Chen, Feng Kong, Weikun Xia, Zili Lin, Sinan Ma, Ling Liu, Xiangguo Wang, Hemin Ni, Wei Li,# Yong Guo,# Wei Xie#. Evolutionary epigenomic analyses in mammalian early embryos reveal species-specific innovations and conserved principles of imprinting. Science Advances. 2021;7(48):eabi6178 (2021).
  14. Jiawei Xu,* # Yimin Shu,* Guidong Yao,# Yu Zhang,* Wenbin Niu, Yile Zhang, Xueshan Ma, Haixia Jin, Fuli Zhang, Senlin Shi, Yang Wang, Wenyan Song, Shanjun Dai, Luyao Cheng, Xiangyang Zhang, Wei Xie,# Aaron J. Hsueh,# and Yingpu Sun.# Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition. Genome Research 2021. 31: 1519-1530 (2021).
  15. Zhenhai Du,* Ke Zhang,* Wei Xie.# Epigenetic Reprogramming in Early Animal Development. Cold Spring Harbor Perspectives in Biology (2021).
  16. Xianglin Zhang,* Xuehui Liu,* Zhenhai Du,* Lei Wei, Huan Fang, Qiongye Dong, Jing Niu, Yanda Li, Juntao Gao, Michael Q Zhang, Wei Xie,# Xiaowo Wang.# The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence.Genome Research 31,1121–35 (2021).
  17. Xiaoxiao Wang,* Yunlong Xiang,* Yang Yu,* Ran Wang, Yu Zhang, Qianhua Xu, Hao Sun, Zhen-Ao Zhao, Xiangxiang Jiang, Xiaoqing Wang, Xukun Lu, Dandan Qin, Yujun Quan, Jiaqi Zhang, Ng Shyh-Chang, Hongmei Wang, Naihe Jing, Wei Xie,#Lei Li.# Formative pluripotent stem cells show features of epiblast cellspoised for gastrulation. Cell Res 31, 526–541 (2021).
  18. Ying Feng,* Yao Wang,* Xiangnan Wang, Xiaohui He, Chen Yang, Ardalan Naseri, Thoru Pederson,Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie,# Hanhui Ma.# Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription.Genome Biol 21, 296 (2020).
  19. Bofeng Liu,* Qianhua Xu,* Qiujun Wang,* Su Feng,* Fangnong Lai, Peizhe Wang, Fangyuan Zheng, Yunlong Xiang, Jingyi Wu, Junwei Nie, Cui Qiu, Weikun Xia, Lijia Li, Guang Yu, Zili Lin, Kai Xu, Zhuqing Xiong, Feng Kong, Ling Liu, Chunyi Huang, Yang Yu, Jie Na, Wei Xie# (2020). The landscape of RNA Pol II binding reveals a step-wise transition during ZGA. Nature (1-6)
  20. Weikun Xia,* Wei Xie# (2020). Rebooting the epigenomes during mammalian early embryogenesis. Stem Cell Reports
  21. Qiujun Wang,* Guang Yu,* Xuan Ming,* Weikun Xia, Xiguang Xu, Yu Zhang, Wenhao Zhang, Yuanyuan Li, Chunyi Huang, Hehuang Xie, Bing Zhu,# Wei Xie# (2020). Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance. Nature Genetics 52 (828-839).
  22. Ke Zhang,* Dan-Ya Wu,* Hui Zheng,* Yao Wang,* Qiao-Ran Sun, Xin Liu, Li-Yan Wang, Wen-Jing Xiong, Qiujun Wang, James D. P. Rhodes, Kai Xu, Lijia Li, Zili Lin, Guang Yu, Weikun Xia, Bo Huang, Zhenhai Du, Yao Yao, Kim A. Nasmyth, Robert J. Klose, Yi-Liang Miao,# Wei Xie# (2020). Analysis of genome architecture during SCNT reveals a role of cohesin in impeding minor ZGA. Molecular Cell 79 (234-250).
  23. Yunlong Xiang,* Yu Zhang,* Qianhua Xu, Chen Zhou, Bofeng Liu, Zhenhai Du, Ke Zhang, Bingjie Zhang, Xiaoxiao Wang, Srimonta Gayen, Ling Liu, Yao Wang, Yuanyuan Li, Qiujun Wang, Sundeep Kalantry, Lei Li & Wei Xie # (2019) Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency. Nature Genetics 52 (95-105).
  24. Zhenhai Du,* Hui Zheng,* Yumiko K.Kawamura,* KeZhang,* Johanna Gassler, Sean Powell, Qianhua Xu, Zili Lin, Kai Xu, QianZhou, Evgeniy A.Ozonov, Nathalie Véron, Bo Huang, Lijia Li, Guang Yu, Ling Liu, Wan Kin Au Yeung, Peizhe Wang, Lei Chang, Qiujun Wang, Aibin He, Yujie Sun, Jie Na, Qingyuan Sun, Hiroyuki Sasaki, Kikuë Tachibana, Antoine H.F.M.Peters,# Wei Xie # (2019) Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos. Molecular Cell 77(825-839).
  25. Weikun Xia,* Jiawei Xu,*# Guang Yu,* Guidong Yao,* Kai Xu,** Xueshan Ma,** Nan Zhang,** Bofeng Liu, Tong Li, Zili Lin, Xia Chen, Lijia Li, Qiujun Wang, Dayuan Shi, Senlin Shi, Yile Zhang, Wenyan Song, Haixia Jin Linli Hu, Zhiqin Bu, Yang Wang, Jie Na, Wei Xie # and Ying-Pu Sun # (2019) Resetting histone modifications during human parental-to-zygotic transition. Science 365 (353-360).
  26. Hui Zheng*, Wei Xie # (2019). The role of 3D genome organization in development and cell differentiation. Nature Reviews Molecular Cell Biology 20 (535-550).
  27. Qianhua Xu,* Yunlong Xiang,* Qiujun Wang,* Leyun Wang,* Julie Brind’Amour, Aaron Blair Bogutz, Yu Zhang, Bingjie Zhang, Guang Yu, Weikun Xia, Zhenhai Du, Chunyi Huang, Jing Ma, Hui Zheng, Yuanyuan Li, Chao Liu, Cheryl Lyn Walker, Eric Jonasch, Louis Lefebvre, Min Wu, Matthew Lorincz, Wei Li # , Li Li # , Wei Xie # (2019) SETD2 regulates the maternal epigenome and embryonic development. Nature Genetics 51 (844–856).
  28. Yao Wang,* Hanben Wang,* Yu Zhang,* Zhenhai Du,* Wei Si,* Suixing Fan, Dongdong Qin, Mei Wang, Yanchao Duan, Lufan Li, Yuying Jiao, Yuanyuan Li, Qiujun Wang, Qinghua Shi, Xin Wu # & Wei Xie # (2019) Reprogramming of meiotic chromatin architecture during spermatogenesis. Molecular Cell 73(547-561).
  29. Bingjie Zhang,* Xiaotong Wu,* Wenhao Zhang,* Weimin Shen, Qingrui Sun, Kaili Liu, Yu Zhang, Qiujun Wang, Yuanyuan Li, Anming Meng # , Wei Xie #, (2018) Widespread enhancer dememorization and promoter priming during parental-to-zygotic transition. Molecular Cell 72 (673-686).
  30. Jingyi Wu,* Jiawei Xu,* Bofeng Liu,* Guidong Yao,* Peizhe Wang,* Zili Lin,* Bo Huang, Xuepeng Wang, Tong Li, Senlin Shi, Nan Zhang, Fuyu Duan, Jia Ming, Xiangyang Zhang, Wenbin Niu, Wenyan Song, Haixia Jin, Yihong Guo, Shanjun Dai, Linli Hu, Lanlan Fang, Qiujun Wang, Yuanyuan Li, Wei Li, Jie Na #, Wei Xie # & Yingpu Sun # (2018) Chromatin analysis in human early development reveals epigenetic transition during ZGA. Nature 557 (256–260).
  31. Qianhua Xu, Wei Xie # (2018) Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment. Trends in Cell Biology 28 (3).
  32. Yuanyuan Li,* Hui Zheng,* Qiujun Wang, Chen Zhou, Lei Wei, Xuehui Liu, Wenhao Zhang, Yu Zhang, Zhenhai Du, Xiaowo Wang, Wei Xie # (2018) Genomewide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valley. Genome Biology 19 (18).
  33. Yu Zhang,* Yunlong Xiang,* Qiangzong Yin,* Zhenhai Du,* Xu Peng, Qiujun Wang, Miguel Fidalgo, Weikun Xia, Yuanyuan Li, Zhenao Zhao, Wenhao Zhang, Jing Ma, Feng Xu, Jianlong Wang, Lei Li, Wei Xie # (2018) Dynamic epigenomic landscapes during early lineage specification. Nature Genetics 50 (96-105).
  34. Zhenhai Du, Hui Zheng, Bo Huang, Rui Ma, Jingyi Wu, Xianglin Zhang, Jing He, Yunlong Xiang, Qiujun Wang, Yuanyuan Li, Jing Ma, Xu Zhang, Ke Zhang, Michael Q. Zhang, Juntao Gao, Jesse R. Dixon, Xiaowo Wang, Jianyang Zeng, Wei Xie # (2017) Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature 547 (232-235).
  35. Reinhard Brunmeir*, Jingyi Wu*, Xu Peng, Sun-Yee Kim, Sofi G. Julien, Qiongyi Zhang, Wei Xie # and Feng Xu # (2016) Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis. PLoS Genetics 12(12): e1006474.
  36. Wenhao Zhang,* Weikun Xia,* Qiujun Wang, Aaron Towers, Jiayu Chen, Rui Gao, Yu Zhang, Chia-an Yen, Ah Young Lee, Yuanyuan Li, Chen Zhou, Kaili Liu, Jing Zhang, Xiuqi Chen, Zai Chang, Danny Leung, Shaorong Gao, Yong-hui Jiang, Wei Xie # (2016) Isoform switch of TET1 regulates demethylation and mouse development. Molecular Cell 64 (1-12).
  37. Bingjie Zhang,* Hui Zheng,* Bo Huang,* Wenzhi Li,* Yunlong Xiang, Xu Peng, Jia Ming, Xiaotong Wu, Yu Zhang, Qianhua Xu, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Wenteng He, Chong Li, Bo Chen, Yuanyuan Li, Qiujun Wang, Jing Ma, Qiangzong Yin, Zai Chang, Kehkooi Kee, Anming Meng, Shaorong Gao, Feng Xu, Jie Na # , **Wei Xie **# (2016). Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. Nature 537 (553-557).
  38. Hui Zheng,* Bo Huang,* Bingjie Zhang,* Yunlong Xiang, Zhenhai Du, Qiujun Wang, Yuanyuan Li, Jing Ma, Xu Peng, Zai Chang, Feng Xu, Wei Xie # (2016). Resetting epigenetic memory by reprogramming of histone modifications in mammals. Molecular Cell 63 (1066-1079).
  39. Jingyi Wu,* Bo Huang,* He Chen, Qiangzong Yin, Yang Liu, Yunlong Xiang, Bingjie Zhang, Bofeng Liu, Qiujun Wang, Weikun Xia, Wenzhi Li, Yuanyuan Li, Jing Ma, Xu Peng, Hui Zheng, Jia Ming, Wenhao Zhang, Jing Zhang, Geng Tian, Feng Xu, Zai Chang, Jie Na, Xuerui Yang, Wei Xie # (2016). The landscape of accessible chromatin in mammalian preimplantation embryos. Nature 534 (652-657).
  40. Bo Xia, Dali Han, Xingyu Lu, Zhaozhu Sun, Ankun Zhou, Qiangzong Yin, Hu Zeng, Menghao Liu, Xiang Jiang, Wei Xie, Chuan He & Chengqi Yi (2015). Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nature Methods 12,1047–1050.
  41. 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 (2015). Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature 518, 350-354.
  42. Jesse R. Dixon,* Inkyung Jung,* Siddarth Selvaraj,* Yin Shen, Jessica E. Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie, Yarui Diao, Jing Liang, Huimin Zhao, Victor V. Lobanenkov, Joseph R. Ecker, James A. Thomson & Bing Ren (2015). Chromatin architecture reorganization during stem cell differentiation. Nature 518, 331-336.
  43. Wei Xie #, Bing Ren #(2013) Enhancing Pluripotency and Lineage Specification, Science 341:247-7
  44. Wei Xie, Matthew D. Schultz, Ryan Lister, Zhonggang Hou, Nisha Rajagopal, Pradipta Ray, John W. 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 R. 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 E. Antosiewicz-Bourget, Igor Slukvin, Ron Stewart, Michael Q. Zhang, Wei Wang, James A. Thomson, Joseph R. Ecker, and Bing Ren (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells, Cell 153: 1134-1148.
  45. Wei Xie, Cathy L Barr, Audrey Kim, Feng Yue, Ah Young Lee, James Eubanks, Emma L Dempster and Bing Ren (2012) Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome, Cell 148: 816-831.
  46. Hao Wu, Volkan Coskun, Jifang Tao, Wei Xie, Weihong Ge, Kazuaki Yoshikawa, En Li, Yi Zhang and Yi Eve Sun (2010) Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes, Science 329 (5990): 444-448.
  47. Mark H. Chin, Mike J. Mason, Wei Xie, Stefano Volinia, Mike Singer, Cory Peterson, Gayane Ambartsumyan, Otaren Aimiuwu, Laura Richter, Jin Zhang, Ivan Khvorostov, Vanessa Ott, Michael Grunstein, Neta Lavon, Nissim Benvenisty, Carlo M. Croce, Amander T. Clark, Tim Baxter, April D. Pyle, Mike A. Teitell, Matteo Pelegrini, Kathrin Plath and William E. Lowry (2009) Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression Signatures, Cell Stem Cell 5(1): 111-123.
  48. Wei Xie, Chunying Song, Nicolas L. Young, Adam Sperling, Feng Xu, Rupa Sridharan, Anne Conway, Benjamin A. Garcia, Kathrin Plath, Amander Clark and Michael Grunstein (2009) Histone H3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells, Molecular Cell, 33(4):417-427.
  49. Roberto Ferrari, Matteo Pellegrini, Gregory A. Horwitz, Wei Xie, Arnold J. Berk and Siavash K. Kurdistani (2008) Epigenetic reprogramming by adenovirus e1a, Science 321, 1086-1088.
  50. Nimet Maherali,* Rupa Sridharan,* Wei Xie, Jochen Utikal, Sarah Eminli, Katrin Arnold, Matthias Stadtfeld, Robin Yachechko, Jason Tchieu, Rudolf Jaenisch, Kathrin Plath and Konrad Hochedlinger (2007) Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution, Cell Stem Cell, 1(1): 55-70.
  51. Feng Xu, Qiongyi Zhang, Kangling Zhang, Wei Xie and Michael Grunstein (2007) Sir2 deacetylates histone H3 lysine 56 to regulate telomeric heterochromatin structure in yeast, Molecular Cell, 27(6): 890-900.