履历

l 2022 – 至今，澳门十大赌博正规官网南强重点岗位教授

l Professor, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.

l 2012 – 2021，澳门十大赌博正规官网教授、院长

l Professor，Dean, College of the Environment and Ecology, Xiamen University.

l 2010 - 2015，美国迈阿密大学，植物学系（后为生物学系），教授（Tenured）

l Professor, Botany Department (Department of Biology), Miami University, Oxford, Ohio.

l 2007 - 2010，美国迈阿密大学，植物学系，副教授（Tenured）

l Associate Professor, Botany Department, Miami University.

l 2001 - 2007/，美国迈阿密大学，植物学系，助理教授

l Assistant Professor, Botany Department, Miami University.

l 1996 - 2001，美国肯塔基大学，烟草研发中心，研究员

l Staff Scientist III and Principal Investigator, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky.

l 1988 - 1991，澳门十大赌博正规官网，生物系，讲师

l Lecturer, Department of Biology, Xiamen University, Xiamen, Fujian, P. R. China.

l 1986/09 - 1988/11，澳门十大赌博正规官网，生物系，助教

l Assistant Professor, Department of Biology, Xiamen University.

l 1995 - 1996，美国肯塔基大学，植物生理/分子生物学，博士后，导师：Arthur G. Hunt.  Postdoctoral Scholar, Plant Physiology/ Biochemistry/ Molecular Biology Program, University of Kentucky, Lexington, Kentucky. Advisor: Arthur G. Hunt

l 1991- 1995，美国肯塔基大学，植物分子生物学/生物化学，哲学博士，导师：Arthur G. Hunt

l Ph.D., Molecular Biology and Biochemistry, University of Kentucky, Lexington, Kentucky, USA. Advisor: Arthur G. Hunt

l 1983- 1986，澳门十大赌博正规官网，生化遗传，理学硕士，导师：黄厚哲

l Master of Science, Biochemical Genetics, Xiamen University. Advisor: Houzhe Huang

l 1979 - 1983，澳门十大赌博正规官网，植物学，理学学士

l Bachelor of Science, Biology (Plant Science), Xiamen University.

研究方向

l 植物基因表达调控中mRNA多聚腺苷化的作用；红树植物环境适应性的分子生态学。

l Plant mRNA polyadenylation in gene expression regulation；Molecular ecology of mangrove adaption.

代表性论文

环境适应性及分子生态学研究 Environment Adaptation and Molecular Ecology

1. Xiaoxuan Zhou, Yulin Weng, Wenyue Su, Congting Ye, Haidong Qu, Qingshun Q. Li*. 2023. Uninterrupted embryonic growth leading to viviparous propagule formation in mangrove. Frontiers in Plant Science. 13:1061747. https://doi.org/10.3389/fpls.2022.1061747

2. Saiqi Hao, Wei Hu, Congting Ye, Yingjia Shen, Qingshun Q. Li*. 2022. Plastid development of albino viviparous propagules in woody mangrove Kandelia obovata. Tree Physiology, 42(11):2353-2368. https://doi.org/10.1093/treephys/tpac063

3. Zejun Guo, Dongna Ma, Jing Li, Mingyue Wei, Ludan Zhang, Lichun Zhou, Xiaoxuan Zhou, Shanshan He, Lin Wang, Yingjia Shen*, Qingshun Q. Li*, Hai-Lei Zheng*. 2022. Genome-wide identification and characterization of aquaporins in mangrove plant Kandelia obovata and its role in response to coastal intertidal environment. Plant, Cell & Environment, 45(6):1698-1718. DOI: 10.111/pce.14286.

4. Saiqi Hao, Wenyue Su, Qingshun Q. Li*. 2021. Adaptive roots of mangrove Avicennia marina: structure and gene expression analyses of pneumatophores. Science of the Total Environment. 757:143994. DOI: 10.1016/j.scitotenv.2020.143994

5. Yuan-Ye Zhang*, Junjie Yin, Ming Zhou, Zeru Lin, Qingshun Q. Li. Adaptive transgenerational effects remain significant. Ecology Letter, in press, July 17, 2020. DOI:10.22541/au.159493093.33229248.

6. Junjie Yin, Ming Zhou, Zeru Lin, Qingshun Q. Li, Yuan-Ye Zhang*. Transgenerational effects benefit offspring across diverse environments: a meta‐analysis in plants and animals. Ecology Letter, 2019, 22: 1976–1986. https://doi.org/10.1111/ele.13373

7. Hongmei Qiao^#, Wenwen Liu^#, Yihui Zhang*, Yuanye Zhang*, Qingshun Q. Li*. Genetic admixture accelerates invasion via provisioning rapid adaptive evolution, Molecular Ecology, 2019, 28:4012-4027. https://doi.org/10.1111/mec.15192

8. Wenyue Su, Congting Ye, Yihui Zhang, Saiqi Hao, Qingshun Q. Li*. Identification of putative key genes for coastal environments and cold adaptation in mangrove Kandelia obovate through transcriptome analysis. Science of the Total Environment, 2019, 681:191–201. DOI: 10.1016/j.scitotenv.2019.05.127

9. Liwei Hong, Wenyue Su, Yuanye Zhang, Congting Ye, Yingjia Shen, Qingshun Q. Li*. 2018. Transcriptome profiling during mangrove viviparity in response to abscisic acid. Scientific Reports, 8:770. DOI:10.1038/s41598-018-19236-x.

10. Xiaoxuan Zhou, Lingling Cai, Meiping Fu, Liwei Hong, Yingjia Shen, Qingshun Q. Li*, 2016. Progress in the Studies of Vivipary on Mangrove Plants. Chinese Journal of Plant Ecology 40(12):1328-1343. 周晓旋, 蔡玲玲, 傅梅萍, 洪礼伟, 沈英嘉, 李庆顺*. 2016. 红树植物胎生现象研究进展, 植物生态学报, 40(12):1328-1343. (In Chinese with English abstract) Doi:10.17521/cjpe.2016.0087.

信使RNA多聚腺苷化机理机制研究 mRNA Polyadenylation Mechanisms

1. Juncheng Lin, Qingshun Q. Li*. 2023. Coupling epigenetic and mRNA polyadenylation: missing links. Trends in Plant Science (invited review), 28(2):223-234. https://doi.org/10.1016/j.tplants.2022.08.023

2. Hui Ma, Juncheng Lin, Fangming Mei, Hude Mao*, Qingshun Q. Li*. 2023. Differential alternative polyadenylation of homoeologous genes of wheat ABD subgenomes during drought response. Plant Journal, 114, 499–518. https://doi.org/10.1111/tpj.16150

3. Zhibo Yu, Liwei Hong, Qingshun Q. Li*. 2022. Signatures of mRNA alternative polyadenylation in Arabidopsis leaf development. Frontiers in Genetics. 13:863253. DOI: 10.3389/fgene.2022.863253.

4. Hui Ma^#, Lingling Cai^#, Juncheng Lin, Kaiyue Zhou, Qingshun Q. Li*. 2022. Divergence in the regulation of the salt tolerant response between Arabidopsis thaliana and its halophytic relative Eutrema salsugineum by mRNA alternative polyadenylation. Frontiers in Plant Science. 13:866054. DOI: 10.3389/fpls.2022.866054

5. Runxuan Zhang*, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, Linda Milne, Stefan Riegler, Akihiro Matsui, Maho Tanaka, Sarah Harvey, Gao Yubang, Theresa Wießner-Kroh, Alejandro Paniagua, Martin Crespi, Katherine Denby, Asa ben Hur, Enamul Huq, Michael F. Jantsch, Artur Jarmolowski, Tino Koester, Sascha Laubinger, Qingshun Q. Li, Lianfeng Gu, Motoaki Seki, Dorothee Staiger, Ramanjulu Sunkar, Zofia Szweykowska-Kulinska, Shih-Long Tu, Andreas Wachter, Robbie Waugh, Liming Xiong, Xiao-Ning Zhang, Ana Conesa, Anireddy S.N. Reddy, Andrea Barta, Maria Kalyna, John WS Brown. 2022. A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23:149. https://doi.org/10.1186/s13059-022-02711-0.

6. Li-Yuan You^#, Juncheng Lin^#, Hua-Wei Xu, Chun-Xiang Chen, Jun-Yu Chen, Jinshan Zhang, Jian Zhang, Ying-Xin Li, Congting Ye, Hui Zhang, Jing Jiang, Jian-Kang Zhu, Qingshun Q. Li^*, Cheng-Guo Duan^*. 2021. Intragenic Heterochromatin-mediated Alternative Polyadenylation Modulates MiRNA Abundance and Pollen Development in Rice. New Phytologist，232: 835–852.DOI:10.1111/nph.17635

7. Congting Ye*, Danhui Zhao, Wenbin Ye, Xiaohui Wu, Guoli Ji, Qingshun Q. Li, Juncheng Lin*. 2021. QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering. Briefings in Bioinformatics, 22(6):bbab268. DOI: 10.1093/bib/bbab268

8. Juncheng Lin^#, Zhibo Yu^#, Liwei Hong, Yiru Chu, Yingjia Shen, Qingshun Q. Li*. 2021. Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis. RNA Biology, 8(12):2594-2604. DOI: 10.1080/15476286.2021.1933732

9. Yi-Zhe Zhang^#, Juncheng Lin^#, Zhizhong Ren^#, Chun-Xiang Chen^#, Daisuke Miki^#, Si-Si Xie, Jian Zhang, Ya-Nan Chang, Jing Jiang, Qingshun Q. Li^*, Jian-Kang Zhu^*, Cheng-Guo Duan^*. 2021. Genome‐wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis, Journal of Integrative Plant Biology, 63(4):707-722. DOI: 10.1111/jipb.13068

10. Juncheng Lin#, Fu-Yu Hung#, Congting Ye, Liwei Hong, Yuan-Hsin Shih, Keqiang Wu*, Qingshun Q. Li*. 2020. HDA6 dependent chromatin deacetylation orchestrates mRNA polyadenylation. Genome Research, 30:1407–1417. DOI:10.1101/gr.255232.119

11. Xuan Wu#, Jie Wang#, Xiaohui Wu, Qingshun Q. Li*. 2020. Heat shock responsive gene expression modulated by mRNA poly(A) tail length. Frontiers in Plant Science, 11:1255. DOI: 10.3389/fpls.2020.01255.

12. Congting Ye, Juncheng Lin, Qingshun Q. Li*. Discovery of alternative polyadenylation dynamics in single cell types. Computational and Structural Biotechnology Journal, 2020, 18:1012-1019. DOI: 10.1016/j.csbj.2020.04.009.

13. Zhibo Yu, Juncheng Lin, Qingshun Q. Li*. 2019. Transcriptome analyses of FY mutants reveal its role in mRNA alternative polyadenylation. Plant Cell. 31(10):2332-2352. https://doi.org/10.1105/tpc.18.00545

14. Haihui Fu, Peng Wang, Xiaohui Wu, Xiaoxuan Zhou, Guoli Ji, Yingjia Shen, Yahui Gao, Qingshun Q. Li*, Junrong Liang*. 2019. Distinct genome‐wide alternative polyadenylation during the response to silicon availability in the marine diatom Thalassiosira pseudonana. Plant Journal. 99(1):67-80. DOI: 10.1111/tpj.14309

15. Congting Ye, Qian Zhou, Xiaohui Wu, Guoli Ji, Qingshun Q. Li*. 2019. Genome-wide alternative polyadenylation dynamics in response to biotic and abiotic stresses in rice. Ecotoxicology and Environmental Safety.183:109485. DOI: 10.1016/j.ecoenv.2019.109485.

16. Congting Ye*, Qian Zhou*, Xiaohui Wu, Chen Yu, Guoli Ji, Daniel R Saban, Qingshun Q. Li. 2019. scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz701

17. Congting Ye, Qian Zhou, Yiling Hong, Qingshun Q. Li*. 2019.Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution. RNA Biology. 16:6, 785-797. DOI: 10.1080/15476286.2019.1586139

18. Qian Zhou, Haihui Fu, Dewei Yang, Congting Ye, Sheng Zhu, Juncheng Lin, Wenbin Ye, Guoli Ji, Xinfu Ye, Xiaohui Wu*, Qingshun Q. Li*. 2019. Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica. Plant Journal. 98,260-276. https://doi.org/10.1111/tpj.14209.

19. Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt, Qingshun Q. Li*. 2019. Root hair single cell type specific profiles of gene expression and alternative polyadenylation under cadmium stress. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.00589

20. Zhixin Zhao, Xiaohui Wu, Guoli Ji, Chun Liang, Qingshun Q. Li*. 2019. Genome-wide comparative analyses of polyadenylation signals in eukaryotes suggest a possible origin of the AAUAAA signal. International Journal of Molecular Sciences. 20(4): 958. Doi: 10.3390/ijms20040958.

21. Congting Ye, Yuqi Long, Guoli Ji, Qingshun Q. Li*, Xiaohui Wu*. 2018. APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics, 34(11):1841-1849. DOI:10.1093/bioinformatics/bty029

22. Liwei Hong, Congting Ye, Juncheng Lin, Haihui Fu, Xiaohui Wu and Qingshun Q. Li*. 2018. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant Journal, 93:246-258. doi: 10.1111/tpj.13771.

23. Juncheng Lin, Ruqiang Xu, Xiaohui Wu, Yingjia Shen and Qingshun Q. Li*. 2017. Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination. Plant Journal, 91:829–839. DOI: 10.1111/tpj.13611

24. Haihui Fu, Dewei Yang, Wenyue Su, Liuyin Ma, Yingjia Shen, Guoli Ji, Xinfu Ye*, Xiaohui Wu*, Qingshun Q. Li*. 2016. Genome-wide Dynamics of Alternative Polyadenylation in Rice. Genome Research, 26: 1753-1760. Doi:10.1101/gr.210757.116

25. Xiaohui Wu*, Yumin Zhang, Qingshun Q. Li *. 2016. PlantAPA: a portal for visualization and analysis of alternative polyadenylation in plants.  Frontiers in Plant Science, 7:889. doi: 10.3389/fpls.2016.00889.

26. Man Liu, Ruqiang Xu, Carrie Merrill, Liwei Hong, Carol Von Lanken, Arthur G. Hunt* and Qingshun Q. Li*. 2014. Integration of developmental and environmental signals via a polyadenylation factor in plants. PloS One. 9: e115779. doi:10.1371/journal.pone.0115779.

27. Liuyin Ma, Pratap Kumar Pati, Man Liu, Qingshun Q. Li* and Arthur G. Hunt*. 2014. High throughput characterizations of poly(A) site choice in plants. Methods. 67:74-83. http://dx.doi.org/10.1016/j.ymeth.2013.06.037

28. Liuyin Ma, Cheng Guo and Qingsun Q. Li*. 2014. Role of alternative polyadenylation in epigenetic silencing and antisilencing. Proc. Nat. Acad. Sci. USA, 111:9-10. DOI: 10.1073/pnas.1321025111

29. Denghui Xing, Yajun Wang, Ruqiang Xu, Xinfu Ye, Dewei Yang, Qingshun Q. Li*. 2013. The Regulatory Role of Pcf11-Similar-4 (PCFS4) in Arabidopsis Development by Genome-Wide Physical Interactions with Target Loci. BMC Genomics. 14:598. DOI:10.1186/1471-2164-14-598

30. Patrick E. Thomas, Xiaohui Wu, Man Liu, Bobby Gaffney, Guoli Ji, Qingshun Q. Li and Arthur G. Hunt*. 2012. Genome-wide control of poly(A) site choice by CPSF30 in Arabidopsis. Plant Cell. 24: 4376-4388. DOI:10.1105/tpc.112.096107

31. Arthur G. Hunt, Denghui Xing*, Qingshun Q. Li*. 2012. Plant polyadenylation factors: conservation and variety. BMC Genomics. 13:641. DOI: 10.1186/1471-2164-13-641

32. Hongwei Zhao, Jun Zheng, Qingshun Q. Li*. 2011. A novel plantin vitro assay system for pre-mRNA cleavage and polyadenylation. Plant Physiology, 157:1546-1554. DOI: 10.1104/pp.111.179465

33. Yingjia Shen, R. C. Venu, Kan Nobuta, Xiaohui Wu, Varun Notibula, Caghan Demirci, Blake C Meyers, Guo-Liang Wang, Guoli Ji, Qingshun Q. Li*. 2011. Transcriptome Dynamics Through Alternative Polyadenylation in Developmental and Environmental Responses in Plants Revealed by Deep Sequencing. Genome Research, 21:1478-1486. DOI: 10.1101/gr.114744.110

34. Xiaohui Wu, Man Liu, Bruce Downie, Chun Liang, Guoli Ji, Qingshun Q. Li*, Arthur Hunt*. 2011. The genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc. Nat. Acad. Sci. USA, 108:12533–12538. doi/10.1073/pnas.1019732108

35. Denghui Xing, Qingshun Q. Li*. 2011. Alternative polyadenylation and gene expression regulation in plants. WIREs (Willey Interdisciplinary Reviews) RNA, 2:445-458. (Invited review) DOI: 10.1002/wrna.59

36. Hongwei Zhao, Denghui Xing, Qingshun Q. Li*.  2009. Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies. Plant Physiology, 151:1546-1556. DOI: 10.1104/pp.109.142729

37. Denghui Xing, Hongwei Zhao and Qingshun Q. Li*. 2008. Arabidopsis CLP1-Similar Protein3, an ortholog of human polyadenylation factor CLP1, functions in gametophyte, embryo and post-embryonic development. Plant Physiology, 148:2059-2069. doi/10.1104/pp.108.129817

38. Yingjia Shen, Yuansheng Liu, Lin Liu, Chun Liang, and Qingshun Q. Li*. 2008. Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics,179:167-176. DOI: 10.1534/genetics.108.088971

39. Denghui Xing, Hongwei Zhao, Ruqiang Xu and Qingshun Q. Li*. 2008. Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p, regulates FCA alternative processing and promotes flowering time. Plant Journal, 54:899-910. DOI: 10.1111/j.1365-313X.2008.03455.x

40. Arthur G. Hunt*, Ruqiang Xu, Balasubrahmanyam Addepalli, Suryadevara Rao, Kevin P. Forbes, Lisa R. Meeks, Denghui Xing, Min Mo, Hongwei Zhao, Amrita Bandyopadhyay, Lavanya Dampanaboina, Amanda Marion, Carol Von Lanken, and Qingshun Q. Li*. 2008. Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling. BMC Genomics, 9:220. DOI: 10.1186/1471-2164-9-220 Highly Accessed

41. Yingjia Shen, Guoli Ji, Brian J. Haas, Xiaohui Wu, Jianti Zheng, Greg J. Reese, and Qingshun Q. Li*. 2008. Genome level analysis of rice mRNA 3’-end processing signals and alternative polyadenylation. Nucleic Acids Research, 36:3150-3161. DOI: 10.1093/nar/gkn158

42. Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, Ronghan Jiang, Yun Lin, Johnny C. Loke, Kimberly M. Davis, Greg J. Reese and Qingshun Q. Li*.  2007. Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics, 8:43. DOI: 10.1186/1471-2105-8-43 Highly Accessed

43. Kim Delaney, Ruqiang Xu, Jingxian Zhang, Qingshun Q. Li, Kil-Young Yun, Deane L. Falcone and Arthur G. Hunt*. 2006. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsispolyadenylation factor subunit. Plant Physiology, 140:1507-1521. DOI: 10.1104/pp.105.070672

44. Ruqiang Xu, Hongwei Zhao, Randy Dinkins, Xiaowen Cheng, George Carberry and Qingshun Q. Li*. 2006. The 73 kD subunit of the cleavage and polyadenylation specificity factor (CPSF) complex affects reproductive development in Arabidopsis.  Plant Molecular Biology, 61:799-815. DOI: 10.1007/s11103-006-0051-6

45. Johnny C. Loke, Eric Stahlberg, Dave Strenski, Brian J. Haas, P. Chris Wood and Qingshun Q. Li*. 2005. Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures. Plant Physiology, 138: 1457-1468. DOI: 10.1104/pp.105.060541

书 BOOK

1. Arthur G. Hunt, Qingshun Q. Li (Editors). 2015. Book title: Polyadenylation in Plants: Methods and Protocols. Series title: Methods in Molecular Biology, Vol 1255. ISSN: 1064-3745; ISBN: 978-1-4939-2174-4. Series Editor: John Walker.  Humana Press, Springer Publishing Group, USA. DOI: 10.1007/978-1-4939-2175-1.

   
   

开设课程

l 分子生物学基础，分子生态学，遗传与进化，生态之美，环境与生态组学技术，生态系统与全球变化

l Molecular Biology, Molecular Ecology, Genetic, Beauty of Ecosystem, Omics Technologies in Environment and Ecology，Ecosystem and Global Change.

科研课题

l 国家重点研发计划，政府间国际科技创新合作重点专项，“通过调控RNA加工因子表达促进作物再生技术研究，2016至2019。

l Chinese Ministry of Science and Technology, National Key Research Project US-Sino Program “Promotion of secondary growth by manipulation of a RNA processing factor”。

l 福建省科学技术厅，福建省对外合作项目，“海岸带卫士红树林植物胎生机制研究及应用”，2016至2019。

l Fujian Department of SciTech Foreign Collaboration Project “Mechanism of Mangrove Vivipary”.

l 国家海洋局，“海洋生态文明中心科研项目”，2014至2015。 Chinese National Bureau of Oceanography “Ocean Eco-civilization Projects”.  

l 厦门市海洋渔业局，下潭尾红树林湿地生态系统监测 2021-

l Ocean and Fishery Bureau of Xiamen: Ecosystem monitoring of restored mangrove wetland ecosystem at Xiatanwei.

l 国家自然科学基金面上项目, 选择性多聚腺苷化对水稻花粉发育与高温胁迫响应的基因表达调控机制研究，2023 – 2026。

l Chinese NSF: The role of alternative polyadenylation on rice pollen heat stress responses.

荣誉奖励

l 美国肯塔基大学植物学系杰出校友奖（2014）。

l Distinguished Alumnus Award, Department of Plant and Soil Sciences, College of Agriculture, Food and Environment, University of Kentucky, 2014.

l 厦门市双百计划人才。

l Xiamen Hundred Talents Plan Awardee, 2013.

l 福建省高层次引进创新创业人才。

l Fujian Provincial Hundred Talents Plan Awardee, 2012 – 2015.

l 迈阿密大学“杰出学者”（2012）。

l Distinguished Scholar, Miami University, 2012.

l Sigma Xi-全美科学研究协会评为“最佳研究者”（2011）。

l Researcher of the Year Award, Sigma Xi – Scientific Research Society, 2011, Miami University Chapter.