Yu Zhou (Ph.D.)

Professor at the Department of Biochemistry

College of Life Sciences

Wuhan University

Wuhan, 430072, China

Email: yu.zhou@whu.edu.cn

Lab Homepage: https://zhoulab.whu.edu.cn/

Research and Work Experience:

07/2022 – present, Professor, TaiKang Center for Life and Medical Sciences, Wuhan University

04/2019 – present, Professor, State Key Laboratory of Virology, Wuhan University

08/2015 – present, Professor, Institute of Advanced Studies, Wuhan University

05/2015 – present, Professor, College of Life Sciences, Wuhan University

07/2009 – 05/2015, Postdoc Fellow, Cellular and Molecular Medicine, UC San Diego, USA

Education:

09/2005 – 12/2008, Ph.D. in Biochemistry and Molecular Biology, Wuhan University, China

09/2005 – 12/2008, Ph.D. in Computer Science, University of Paris-Sud 11, France (Joint Ph.D. program with Wuhan University)

10/2004 – 07/2005, Master 2 in Bioinformatics and Biostatistics, University of Paris-Sud 11, Paris, France

09/2003 – 09/2004, Graduate studies in Biochemistry and Molecular Biology, Wuhan University, Wuhan, China

09/1999 – 06/2003, Bachelor, Biological Science, Wuhan University, Wuhan, China

Research Interests:

RNA is a crucial molecule for gene expression in eukaryotes. RNA processing transforms the precursor RNA, transcribed from the DNA template, into mature mRNA or regulatory ncRNA through splicing, polyadenylation, modification, etc. This is essential for the accurate transmission of genetic information. Abnormal RNA processing can lead to a variety of severe diseases like neurodegenerative diseases and cancers. We are a “dry and wet” RNA laboratory focusing on the “regulation and function of RNA processing,” integrating bioinformatic analysis and high-throughput sequencing technologies, and developing new technologies and analytical methods for RNA research. Current research topics include:

1. Developing new technologies to analyze new mechanisms and functions of RNA regulation;

2. Studying the functions of RNA sequential polyadenylation;

3. Investigating the mechanisms and functions of RNA nuclear retention;

4. Developing AI models of RNA processing;

5. Analyzing the pathological roles of abnormal RNA processing in various diseases.

Additionally, we cooperate with other laboratories to address biological problems from a bioinformatics perspective.

Teaching:

2016 – present, Undergraduates, Genomics

2016 – present, Graduates, Functional Genomics

2017 – present, Graduates, Bioinformatics

2017 – 2019, Graduates, Computational Biology

Representative Publications (#First author, *Corresponding author)

1. Peng Tang#, Jiayi Yang#, Zonggui Chen#, Chen Du, Yang Yang, Haiping Zhao, Li Huang, Guangnan Li, Feiyan Liu, Bei Dong, Ting Shan, Xichen Bao, Yu Zhou*. Nuclear retention coupled with sequential polyadenylation dictates post-transcriptional m⁶A modification in the nucleus, Molecular Cell, 2024, 84, DOI: 10.1016/j.molcel.2024.07.017.

2. Xinghai Yu#, Jinghua Zhou#, Wenkai Ye#, Jingxiu Xu, Rui Li, Li Huang, Yi Chai, Miaomiao Wen, Suhong Xu*, Yu Zhou*. Time-course swRNA-seq uncovers a hierarchical gene regulatory network in controlling the response-repair-remodeling after wounding, Communications Biology 2024, 7: 694.

3. Ting Shan#, Feiyan Liu#, Miaomiao Wen#, Zonggui Chen, Shaopeng Li, Yafen Wang, Hong Cheng, Yu Zhou*. m⁶A modification negatively regulates translation by switching mRNA from polysome to P-body via IGF2BP3. Molecular Cell, 2023, 83:4494–4508.

4. Changshou Wang#, Lin Xu#, Chen Du#, Hao Yun#, KeyunWang#, Hui Liu, Mingliang Ye*, Jing Fan*, Yu Zhou*, Hong Cheng*. CDK11 requires a critical activator SAP30BP to regulate pre-mRNA splicing. The EMBO Journal, 2023, 42(24):e114051.

5. Li Huang#, Guangnan Li#, Chen Du#, Yu Jia, Jiayi Yang, Weiliang Fan, YongZhen Xu, Hong Cheng, Yu Zhou*. The polyA tail facilitates splicing of last introns with weak 3’ splice sites via PABPN1. EMBO Reports, 2023, 24:e57128.

6. Dehe Wang#, Xiao Hu#, Hanzhe Ye, Yue Wang, Qian Yang, Xiaodong Liang, Zilin Wang, Yifan Zhou, MiaomiaoWen, Xueyan Yuan, Xiaomin Zheng, Wen Ye, Boyu Guo, Mayila Yusuyin, Eugenia Russinova, Yu Zhou*, Kun Wang*. Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton. Genome Biology, 2023, 24(1):49.

7. Guangnan Li#, Zhidong Tang#, Weiliang Fan#, Xi Wang#, Li Huang, Yu Jia, Manli Wang, Zhihong Hu, Yu Zhou*. Atlas of interactions between SARS-CoV-2 macromolecules and host proteins. Cell Insight, 2023, 2:100068.

8. Kai Wu#, Dehe Wang#, Junhao Wang, Yu Zhou*. Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs. Virologica Sinica, 2022, 37:813–822.

9. Peng Tang#, Yu Zhou*. Alternative polyadenylation regulation: insights from sequential polyadenylation. Transcription, 2022, 13:4-5:89–95.

10. Bingbing Xu#, Yanda Zhu#, Changchang Cao#, Hao Chen#, Qiongli Jin#, Guangnan Li#, Junfeng Ma#, Siwy Ling Yang#, Jieyu Zhao#, Jianghui Zhu#, Yiliang Ding*, Xianyang Fang*, Yongfeng Jin*, Chun Kit Kwok*, Aiming Ren*, Yue Wan*, Zhiye Wang*, Yuanchao Xue*, Huakun Zhang*, Qiangfeng Cliff Zhang*, Yu Zhou*. Recent advances in RNA structurome. Science China Life Sciences, 2022, 65:1285–1324.

11. Geng Chen#, Yang Yang#, Qi-Jia Wu#, Liu Cao#, Wen Ruan, Changwei Shao, Li Jiang, Peng Tang, Suping Ma, Ao Jiang, Zhen Wang, Kai Wu, Qiangfeng Cliff Zhang, Xiang-Dong Fu, Yu Zhou*. ILF3 represses repeat-derived microRNAs targeting RIG-I mediated type I interferon response. Journal of Molecular Biology, 2022, 434(7):167469.

12. Shaopeng Li#, Linmao Li#, Weiliang Fan, Suping Ma, Cheng Zhang, Jang Chol Kim, Kun Wang, Eugenia Russinova, Yuxian Zhu*, Yu Zhou*. LeafNet: a tool for segmenting and quantifying stomata and pavement cells. The Plant Cell, 2022, 34(4):1171–1188.

13. Peng Tang#, Yang Yang#, Guangnan Li, Li Huang, Miaomiao Wen, Wen Ruan, Xiaolong Guo, Chen Zhang, Xinxin Zuo, Daji Luo, Yongzhen Xu, Xiang-Dong Fu*, Yu Zhou*. Alternative polyadenylation by sequential activation of distal and proximal PolyA sites. Nature Structural & Molecular Biology, 2022, 29(1):21–31.

14. Zhidong Tang#, Weiliang Fan#, Qiming Li#, Dehe Wang, Miaomiao Wen, Junhao Wang, Xingqiao Li, Yu Zhou*. MVIP: multi-omics portal of viral infection. Nucleic Acids Research, 2022, 50(D1):D817–D827.

15. Yangyang Li#, Zonggui Chen#, Hairong Liu#, Qiming Li, Xing Lin, Shuhui Ji, Rui Li, Shaopeng Li, Weiliang Fan, Haiping Zhao, Zuoyan Zhu, Wei Hu*, Yu Zhou*, Daji Luo*. ASER: Animal Sex Reversal Database. Genomics Proteomics Bioinformatics, 2021, 19:873–881.

16. Dehe Wang#, Ao Jiang#, Jiangpeng Feng#, Guangnan Li#, Dong Guo#, Muhammad Sajid, Kai Wu, Qiuhan Zhang, Yann Ponty, Sebastian Will, Feiyan Liu, Xinghai Yu, Shaopeng Li, Qianyun Liu, Xing-Lou Yang, Ming Guo, Xingqiao Li, Mingzhou Chen, Zheng-Li Shi, Ke Lan*, Yu Chen*, Yu Zhou*. The SARS-CoV-2 subgenome landscape and its novel regulatory features. Molecular Cell, 2021, 81(10):2135–2147.

17. Xinxin Zuo#, Jie Zhou#, Yinming Li#, Kai Wu, Zonggui Chen, Zhiwei Luo, Xiaorong Zhang, Yi Liang, Miguel A. Esteban, Yu Zhou*, Xiang-Dong Fu*. TDP-43 aggregation induced by oxidative stress causes global mitochondrial imbalance in ALS. Nature Structural & Molecular Biology, 2021, 28:132–142.

18. Yong Xiong#, Yuan Liu#, Liu Cao#, Dehe Wang#, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu, Yu Zhou*, Ke Lan*, Yu Chen*. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Emerging Microbes & Infections 2020, 9, 761–770.

19. Dehe Wang#, Weiliang Fan#, Xiaolong Guo#, Kai Wu, Siyu Zhou, Zonggui Chen, Danyang Li, Kun Wang*, Yuxian Zhu*, Yu Zhou*. MaGenDB: a functional genomics hub for Malvaceae plants. Nucleic Acids Research, 2020, 48: D1076-D1084.

20. Peng Dai#, Xin Wang#, Lan-Tao Gou#, Zhi-Tong Li#, Ze Wen#, Zong-Gui Chen#, Min-Min Hua, Ai Zhong, Lingbo Wang, Haiyang Su, Huida Wan, Kun Qian, Lujian Liao, Jinsong Li, Bin Tian, Dangsheng Li, Xiang-Dong Fu, Hui-Juan Shi*, Yu Zhou*, Mo-Fang Liu*. A Translation-Activating Function of MIWI/piRNA during Mouse Spermiogenesis. Cell, 2019, 179:1566-1581.

21. Kun Wang#, Dehe Wang#, Xiaomin Zheng, Ai Qin, Jie Zhou, Boyu Guo, Yanjun Chen, Xingpeng Wen, Wen Ye, Yu Zhou*, Yuxian Zhu*. Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton. Nature Communications, 2019, 10:4714.

22. Jianshu Wang#, Jiyun Chen#, Guifen Wu#, Hongling Zhang#, Xian Du#, Suli Chen, Li Zhang, Ke Wang, Jing Fan, Shuaixin Gao, Xudong Wu, Shouxiang Zhang, Bin Kuai, Peng Zhao, Binkai Chi, Lantian Wang, Guohui Li, Catherine C.L. Wong, Yu Zhou*, Jinsong Li*, Caihong Yun*, Hong Cheng*. NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction. Genes & Development, 2019, 33:536-549.

23. Kai Zhang#, Xiaorong Zhang#, Zhiqiang Cai#, Jie Zhou#, Ran Cao, Ya Zhao, Zonggui Chen, Dehe Wang, Wen Ruan, Qian Zhao, Guangqiao Liu, Yuanchao Xue, Yan Qin, Bing Zhou, Ligang Wu, Timothy Nilsen, Yu Zhou*, Xiang-Dong Fu*. A novel class of microRNA-recognition elements that function only within open reading frames. Nature Structural & Molecular Biology, 2018, 25(11):1019-1027.

24. Jiaqi Gu#, Ming Wang#, Yang Yang#, Ding Qiu, Yiqun Zhang, Jinbiao Ma*, Yu Zhou*, Gregory J. Hannon*, Yang Yu*. GoldCLIP: Gel-omitted Ligation-dependent CLIP. Genomics, Proteomics & Bioinformatics, 2018, 16(2):136-143.

25. Li Jiang#, Changwei Shao#, Qi-Jia Wu#, Geng Chen, Jie Zhou, Bo Yang, Hairi Li, Lan-Tao Gou, Yi Zhang, Yangming Wang, Gene W Yeo, Yu Zhou*, Xiang-Dong Fu*. NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing. Nature Structural & Molecular Biology, 2017, 24:816-824.

26. Huiwu Ouyang, Kai Zhang, Kristi Fox-Walsh, Yang Yang, Chen Zhang, Jie Huang, Hairi Li, Yu Zhou*, Xiang-Dong Fu*. The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells. Nucleic Acids Research, 2017, 45(21):12481-12495.

27. Chaoliang Wei#, Rui Xiao#, Liang Chen#, Hanwei Cui#, Yu Zhou#, Yuanchao Xue, Jing Hu, Bing Zhou, Taiki Tsutsui, Jinsong Qiu, Hairi Li, Liling Tang, Xiang-Dong Fu*. RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes. Molecular Cell, 2016, 62(6):875-889.

28. Lanfeng Wang#, Yu Zhou#, Liang Xu#, Rui Xiao#, Xingyu Lu, Liang Chen, Jenny Chong, Hairi Li, Chuan He, Xiang-Dong Fu*, Dong Wang*. Molecular Basis for 5-Carboxycytosine Recognition by RNA Polymerase II Elongation Complex. Nature, 2015, 523:621–625.

29. Yu Zhou#, Hai-Ri Li, Jie Huang, Ge Jin, Xiang-Dong Fu*. Multiplex analysis of polyA-linked sequences (MAPS): an RNA-seq strategy to profile poly(A+) RNA. Methods Mol Biol, 2014, 1125:169-178.

30. Shatakshi Pandit#, Yu Zhou#, Lily Shiue#, Gabriela Coutinho-Mansfield, Hairi Li, Jinsong Qiu, Jie Huang, Gene W. Yeo, Manuel Ares, Jr.*, Xiang-Dong Fu*. Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Molecular Cell, 2013, 50(2):223-235.

31. Yu Zhou#, Yann Ponty#, Stephane Vialette, Jerome Waldispuhl, Yi Zhang, Alain Denise*. Flexible RNA design under structure and sequence constraints using formal languages. In ACM BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics. Bethesda, Washington DC, United States, 2013.

32. Yuanchao Xue#, Yu Zhou#, Tongbin Wu, Tuo Zhu, Xiong Ji, Young-Soo Kwon, Chao Zhang, Gene Yeo, Douglas L. Black, Hui Sun, Xiang-Dong Fu*, Yi Zhang*. Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Molecular Cell, 2009, 36(6):996-1006.

33. Yu Zhou#, Chen Lu#, Qi-Jia Wu#, Yu Wang, Zhi-Tao Sun, Jia-Cong Deng, Yi Zhang*. GISSD: Group I Intron Sequence and Structure Database. Nucleic Acids Research, 2008, 36:D31-D37.