1.Daixuan Zhang#, Li Dong#, Ying Cai, Peng Zhao, Qingqing Cai, Jian Zhang, Yajun Hu, Mandi Mu, Siyi Cheng, Jin Wang, Min Zeng, Chenxi He, Lei Zhang, Hui Yang, Fei Xavier Chen, Li Tan, Feizhen Wu, Yujiang Geno Shi, Wenqi Xu*, Hongjie Shen*, SPT6 Regulates H3K14Ac Deposition in Mouse Embryonic Stem Cells, Cell Reports, 2025 May 30,44(6):115757.

2.Li Dong#, Daixuan Zhang#, Ying Cai, Min Zeng, Mandi Mu, Peng Zhao, Jin Wang, Siyi Cheng, Qingqing Cai, Jian Zhang, Yajun Hu, Lei Zhang, Li Tan, Feizhen Wu, Yujiang Geno Shi, Wenqi Xu*, and Hongjie Shen*, RACK7 Senses and Fine-Tunes Enhancer Activity, iSicence, 2025 Jul 9;28(8):113083

3.Chongping Li#,*, Ying Li#, Yuci Wang#, Xiangrui Meng#, Xiaoyan Shi, Yangyi Zhang, Nan Liang, Hongda Huang, Yue Li, Hui Zhou, Jiawei Xu*, Wenqi Xu*, Hao Chen*, Characterization of the enzyme for 5-hydroxymethyluridine production and its role in silencing transposable elements in dinoflagellates, Proc Natl Acad Sci U S A, 2024, 121(46): e2400906121

4.Mandi Mu, Xinze Li, Li Dong, Jin Wang, Qingqing Cai, Yajun Hu, Duanduan Wang, Peng Zhao, Lei Zhang , Daixuan Zhang, Siyi Cheng, Li Tan, Feizhen Wu, Yujiang Geno Shi, Wenqi Xu*, Yang Shi*, Hongjie Shen*. METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells. Cell Reports. 2023 Jun 13;42(6):112650.

5.Wenqi Xu, Jiahui Li, Chenxi He, Jing Wen, Honghui Ma, Bowen Rong, Jianbo Diao, Liyong Wang, Jiahua Wang, Feizhen Wu, Li Tan, Yujiang Geno Shi, Yang Shi*, Hongjie Shen*, METTL3 regulates heterochromatin in mouse embryonic stem cells, Nature. 2021 Mar;591(7849):317-321.

6.Wenqi Xu#, Chenxi He#, Emily G. Kaye, Jiahui Li, Mandi Mu, Geoffrey M. Nelson, Li Dong, Jiahua Wang, Feizhen Wu, Yujiang Geno Shi, Karen Adelman*, Fei Lan*, Yang Shi*, Hongjie Shen*, Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNA Synthesis, Mol Cell, 2022 Mar 17;82(6):1156-1168.e7.

7.Hongjie Shen#, Wenqi Xu#, Rui Guo, Bowen Rong, Lei Gu, Zhentian Wang, Chenxi He, Lijuan Zheng, Xin Hu, Zhen Hu, Zhi-Ming Shao, Pengyuan Yang, Feizhen Wu, Yujiang Geno Shi, Yang Shi*, Fei Lan*, Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex, Cell, 2016 Apr 7;165(2):331-42

8.Wenqi Xu#, Jiahui Li#, Bowen Rong#, Bin Zhao, Mei Wang, Ruofei Dai, Qilong Chen, Hang Liu, Zhongkai Gu, Shuxian Liu, Rui Guo, Hongjie Shen*, Feizhen Wu*, Fei Lan*; DNMT3A reads and connects histone H3K36me2 to DNA methylation. Protein Cell. 2020 Feb;11(2):150-154.

9.Li Tan#, Lijun Xiong#, Wenqi Xu#, Feizhen Wu, Ning Huang, Yufei Xu, Lingchun Kong, Lijuan Zheng, Lisa Schwartz, Yang Shi, Yujiang Geno Shi. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res. 2013 Apr;41(7):e84.

10.Wenqi Xu, Hongjie Shen, When RNA methylation meets DNA methylation. Nat Genet. 2022 Sep;54(9):1261-1262.

11.Wenqi Xu, Hongjie Shen, m⁶A regulates heterochromatin in mammalian embryonic stem cells. Current Opinion in Genetics & Development. 2024 Jun;86:102196

12.Hongjie Shen#, Wenqi Xu#, Fei Lan*. Histone lysine demethylases in mammalian embryonic development. Exp Mol Med. 2017 Apr 28;49(4):e325.

13.Bin Zhao, Wenqi Xu, Bowen Rong, Guoyu Chen, Xuanjia Ye, Ruofei Dai, Wenjing Li, Jiajia Chen, Jiajun Cai, Lei Song, Zhao-Qing Luo, Rong Zeng, Yang Shi, Jing-Dong J Han, Fei Lan. H3K14me3 genomic distributions and its regulation by KDM4 family demethylases. Cell Research, 2018 Nov;28(11):1118-1120.

14.Fangfang Jiao#, Ze Li#, Chen He, Wenqi Xu, Gensheng Yang, Tingting Liu, Hongjie Shen, Jiajun Cai, Jamie N Anastas, Ying Mao, Yongchun Yu, Fei Lan, Yujiang Geno Shi, Chris Jones, Yanhui Xu, Suzanne J Baker*, Yang Shi*, Rui Guo*. RACK7 recognizes H3.3G34R mutation to suppress expression of MHC class II complex components and their delivery pathway in pediatric glioblastoma. Sci Adv. 2020 Jul 17;6(29):eaba2113.

15.Chun Ma, Violetta Karwacki-Neisius, Haoran Tang, Wenjing Li, Zhennan Shi, Haolin Hu, Wenqi Xu, Zhentian Wang, Lingchun Kong, Ruitu Lv, Zheng Fan, Wenhao Zhou, Pengyuan Yang, Feizhen Wu, Jianbo Diao, Li Tan, Yujiang Geno Shi, Fei Lan, Yang Shi. Nono, a Bivalent Domain Factor, Regulates Erk Signaling and Mouse Embryonic Stem Cell Pluripotency. Cell Rep. 2016 Oct 18;17(4):997-1007.

16.Rui Guo, Lijuan Zheng, Juw Won Park, Ruitu Lv, Hao Chen, Fangfang Jiao, Wenqi Xu, Shirong Mu, Hong Wen, Jinsong Qiu, Zhentian Wang, Pengyuan Yang, Feizhen Wu, Jingyi Hui, Xiangdong Fu, Xiaobing Shi, Yujiang Geno Shi, Yi Xing, Fei Lan, Yang Shi. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell. 2014 Oct 23;56(2):298-310.

17.Christine Guo Lian, Yufei Xu, Craig Ceol, Feizhen Wu, Allison Larson, Karen Dresser, Wenqi Xu, Li Tan, Yeguang Hu, Qian Zhan, Chung-Wei Lee, Di Hu, Bill Q Lian, Sonja Kleffel, Yijun Yang, James Neiswender, Abraham J Khorasani, Rui Fang, Cecilia Lezcano, Lyn M Duncan, Richard A Scolyer, John F Thompson, Hojabr Kakavand, Yariv Houvras, Leonard I Zon, Martin C Mihm Jr, Ursula B Kaiser, Tobias Schatton, Bruce A Woda, George F Murphy, Yujiang G Shi. Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell. 2012 Sep 14;150(6):1135-46.

18.Shuzhen Chen, Jian Ma, Feizhen Wu, Li-Jun Xiong, Honghui Ma, Wenqi Xu, Ruitu Lv, Xiaodong Li, Judit Villen, Steven P Gygi, Xiaole Shirley Liu, Yang Shi. The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation. Genes Dev. 2012 Jun 15;26(12):1364-75.