实验室主页：https://zhoulab.whu.edu.cn/

学习经历

1999-09－2003-06 武汉大学 本科 生物学基地班

2003-09－2004-09 武汉大学 硕士 生化与分子生物学

2004-10－2005-07 法国巴黎十一大学 硕士 生物信息与生物统计学

2005-09－2008-12 武汉大学 博士 生化与分子生物学

2005-09－2008-12 法国巴黎十一大学 博士 计算机 (与武汉大学联合培养）

主要工作经历及任职情况

2009-07－2015-05 美国加州大学圣地亚哥分校 博士后

2015-05－至今 武汉大学生命科学学院 教授

2015-08－至今 武汉大学高等研究院 兼职研究员

2019-04－至今 病毒学国家重点实验室 教授
2022-07－至今 泰康生命医学中心　　 教授

主要研究领域及兴趣

RNA是真核生物中基因表达的关键分子。RNA加工将以DNA为模板转录的前体RNA通过剪接、加尾、修饰等步骤，转变为可被翻译的成熟mRNA或具有调控功能的ncRNA，这不但是遗传信息传递的关键环节，也是遗传信息高效、精准传递的基础。RNA加工异常会导致多种严重威胁人类生命健康的重大疾病，包括神经退行性疾病和癌症等。我们是“干湿结合”的RNA实验室，重点围绕“RNA加工的调控与功能”开展研究，融合生物信息分析与高通量测序技术，研发RNA研究新技术和分析方法，当前的研究主题包括：

1. 开发新技术解析RNA调控新机制和功能；

2. RNA渐进式加尾的生理和病理功能；

3. RNA核滞留的机制和功能；

4. 构建RNA加工的AI模型；

5. 解析RNA异常在多种疾病中的致病机理。

同时与其他国内外实验室合作，从生物信息学角度解决多种生物学问题。

教学

2016年秋季－至今 本科生 基因组学

2016年秋季－至今 研究生 功能基因组学

2017年秋季－至今 研究生 生物信息学

2017年春季－2019 研究生 计算生物学

代表性论文（#共同第一作者，*通讯作者）

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.