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Graduate College of Biomedical Sciences

Q. Quinn Li Laboratory

Dr. Ethell in labDr. Qingshun Quinn Li

Professor

Graduate College of Biomedical Sciences

Western University of Health Sciences

Pomona, CA 91766, USA

Phone: 909-469-8523  Fax: 909-469-8750

E-mail: qqli(at)westernu.edu

Office: 113 Daumier

Lab web site: www.polyA.org

Ph.D. (1995) University of Kentucky

Honors / Awards

Best Faculty Mentor Award, Graduate College of Biomedical Sciences, Western University of Health Sciences, 2017.

Distinguished Alumnus, Department of Plant and Soil Sciences, University of Kentucky, 2014.

Distinguished Scholar, Miami University 2012.

Researcher of the Year, Sigma Xi, Miami University 2011.

Research Interests:

Mechanism of mRNA polyadenylation

Messenger RNA polyadenylation is one of the critical steps in eukaryotic gene expression. The poly(A) tail of a mature mRNA is essential for its function, including mRNA translatability, stability and translocation to cytoplasm. The process also affects pre-mRNA splicing and transcription termination. Recent studies have linked mRNA polyadenylation to other cellular processes, e.g. pathogen invasion and cancer development. In plants, it has been shown that the polyadenylation process, and the alternative polyadenylation of mRNA, can lead to gene expression regulation. In particular, alternative polyadenylation of certain genes plays an important role in many biological processes like flower development, self-incompatibility, stress responses, etc.

I am interested to elucidate plant mRNA polyadenylation mechanisms at genetic, biochemical, and molecular levels. We have used bioinformatics and molecular biology approaches to identify and clone plant (Arabidopsis) polyadenylation related genes. Funded by US National Science Foundation’s Arabidopsis 2010 Project, we use functional genomic tools to study the functions of this set of genes. Funded by US National Science Foundation and US National Instate of Health, we are studying the biochemical, genetic and molecular functions of some polyadenylation factors, and their role in plant gene expression regulations in gametophyte development and stress responses.

It has been demonstrated in recent years that alternative polyadenylation, a process that generates a few poly(A) sites on different transcripts of a gene, is a widely used post-transcriptional molecular mechanism in gene expression regulation, including cancer development, embryo development and stress responses. Since the poly(A) site marks the end of a transcript, different placements of a poly(A) site may include or exclude coding sequences, regulatory cis-elements (micro RNA targets, stability elements, etc). Thus, regulated placements of poly(A) sites can be a strategy for gene expression regulation. We are performing large-scale analyses of alternative polyadenylation to discover the full landscape of polyadenylation in plants. The emergent theme is that over 70% genes use alternative polyadenylation to regulate their expression.

The cis-elements which direct the plant mRNA polyadenylation process are not well understood yet. We are using bioinformatics tools to search and analyze such polyadenylation signals in the plant genomes, and building models and algorithms to predict poly(A) sites. This exercise has two major applications: genome annotation by predicting the end of a transcript and transcription termination, and prediction of unwanted poly(A) sites for candidate genes to be transformed to plants. The latter can be used to guide gene modification to ensure desired expression in plants.

Role of mRNA processing in stem cell differentiation

Our research interests have been extended to study the role of RNA processing in human and animal stem cell differentiation.  This includes transcriptome level analysis of gene expression regulation through post-transcriptional means like mRNA polyadenylation and splicing.  The Poly(A)-tag sequencing (PAT-Seq) techniques and data processing pipelines development by us are used to assess gene expression during stem cell differentiation into different cell linages.  The impact of environmental factors like nanoparticles and pollutants on stem cell functions is also under study.   

Selected Publications (*corresponding author)

2018

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, in press. DOI:10.1093/bioinformatics/bty029

Neza Repar, Hao Li, Jose S. Aguilar, Qingshun Q. Li, Drobne Damjana, and Yiling Hong*. 2018. Silver nanoparticles induced neurotoxicity in neuron and astrocyte network derived from human embryonic stem cells. Nanotoxicology, 12:104-116.  DOI: 10.1080/17435390.2018.1425497

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.

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.

2017

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 Terminating Transcription in Arabidopsis. Plant Journal, 91:829–839. DOI: 10.1111/tpj.13611

Luzhen Chen*, Wenqing Wang, Qingshun Q. Li, Yihui Zhang, Shengchang Yang, Michael J. Osland, Jinliang Huang, and Congjiao Peng. 2017. Mangrove species’ responses to winter air temperature extremes in China. Ecosphere, 8(6): e01865. DOI: 10.1002/ecs2.1865

Cheng Guo, Matthew Spinelli, Congting Ye, Qingshun Q. Li* and Chun Liang*. 2017. Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Element in 19 Arabidopsis thaliana Accessions. Scientific Reports, 7:2634. DOI: 10.1038/s41598-017-02855-1.

Qingshun Q. Li*, Zhaoyang Liu, Wenjia Lu and Man Liu. 2017. Interplay between Alternative Splicing and Alternative Polyadenylation Defines the Expression Outcome of the Plant Unique OXIDATIVE TOLERANT-6 Gene. Scientific Reports, 7:2052. DOI: 10.1038/s41598-017-02215-z

Kristopher J. L. Irizarry*, Adam Chan, Derek Kettle, Steven Kezian, Dominic Ma, Louis Palacios, Q. Quinn Li, Calvin L. Keeler and Yvonne Drechsler. Bioinformatics Analysis of Chicken miRNAs Associated with Monocyte to Macrophage Differentiation and Subsequent IFN Stimulated Activation. MicroRNA, 6:1-19. DOI:10.2174/2211536605666161129122803.

2016

Xiao-xuan Zhou, Ling-ling Cai, Mei-ping Fu, Li-wei Hong, Ying-jia Shen, Qingshun Q. Li*, 2016. Progress in the Studies of Vivipary on Mangrove Plants. Chinese Journal of Plant Ecology 40(12):1328-1343. (In Chinese with English abstract) Doi:10.17521/cjpe.2016.0087

Haihui Fu, Dewei Yang, Wenyue Su, Liuyin Ma, Yingjia Shen, Guoli Ji, Xinfu Ye*, Xiaohui Wu*, Q. Quinn Li*. 2016. Genome-wide Dynamics of Alternative Polyadenylation in Rice. Genome Research, 26: 1753-1760. Link to Abstract 

Xiaohui Wu*, Yumin Zhang, Q. Quinn 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. Download paper

Cheng Guo, Matthew Spinelli, Man Liu, Q. Quinn Li* and Chun Liang*. 2016. A Genome-wide Study of “Non-3UTR” Polyadenylation Sites in Arabidopsis thaliana. Scientific Report, 6:28060; doi: 10.1038/srep28060 (2016). Download paper

Dewei Yang, Xinfu Ye*, Xianghua Zheng, Chaoping Cheng, Ning Ye, Libin Lu, Fenghuang Huang, Q Quinn Li*.  2016. Identification and fine mapping of LD1, a single recessive gene playing an essential role in the development of lemma in rice. J. Agricultural Science 154(6)989-1001. DOI:10.1017/S0021859615000866

2015

Xiaohui Wu*, Yong Zeng, Jinting Guan, Guoli, Ji, Rongting Huang, Q. Quinn Li*. 2015. Genome-wide Characterization of Intergenic Polyadenylation Sites Redefines Gene Spaces in Arabidopsis thaliana. BMC Genomics. 16:511. DOI: 10.1186/s12864-015-1691-1 Download paper

Guoli Ji, Jinting Guan, Yong Zeng, Q. Quinn Li and Xiaohui Wu*. 2015. Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes.  Briefings in Bioinformatics. 16(2): 304-313. DOI: 10.1093/bib/bbu011 Download abstract

Guoli Ji, Lei Li, Q. Quinn Li, Xiangdong Wu, Jingyi Fu, Xiaohui Wu*. 2015. PASPA: a web server for mRNA poly(A) site predictions in plants and algae. Bioinformatics, 31(10): 1671-3. doi:10.1093/bioinformatics/btv004. Download abstract

Jinting Guan, Jingyi Fu, Mingcheng Wu, Longteng Chen, Guoli Ji, Q. Quinn Li, Xiaohui Wu*. 2015. VAAPA: A web platform for visualization and analysis of alternative polyadenylation. Comput Biol Med. 57:20-25. doi: 10.1016/j.compbiomed.2014.11.010 Download abstract

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

   2015 Book chapters

Jingyi Cao, Q. Quinn Li*. 2015. Poly(A) Tag Library Construction from 10 ng Total RNA.  Pp185-194. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Hongwei Zhao*, Xinfu Ye, Q. Quinn Li.. 2015. Characterization of plant polyadenylation complexes by using tandem affinity purification.  Pp 69-78. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA. 

Hongwei Zhao*, Q. Quinn Li. 2015. In vitro analysis of cleavage and polyadenylation in Arabidopsis. Pp 79-90. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Denghui Xing*, Q. Quinn Li. 2015. RADPRE: a computational program for identification of differential mRNA processing including alternative polyadenylation. Pp 57- 68. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Xiaohui Wu, Guoli Ji, Q. Quinn Li*. 2015. Computational analysis of plant polyadenylation signals. Pp 3-12. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Xiaohui Wu*, Guoli Ji, Q. Quinn Li. 2015. Prediction of plant polyadenylation sites. Pp 13-24. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Xiaohui Wu*, Guoli Ji, Q. Quinn Li. 2015. Poly(A) Tag deep sequencing data processing to extract poly(A) sites. Pp 39-48. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Min Dong, Q. Quinn Li, and Chun Liang*.  2015. Extraction of poly(A) sites from RNA-seq data. Pp 25-38. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Man Liu, Xiaohui Wu, Q. Quinn Li*.  2015. DNA/RNA hybrid primer mediated poly(A) tag library construction for Illumina sequencing. Pp 175-184. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li.  Series: Methods in Molecular Biology Vol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

2014

Xiaohui Wu, Bobby Gaffney, Arthur G. Hunt*, and Q. Quinn Li *. Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 15:615. Download paper

William C Ray*, Samuel L Wolock, Nicholas W Callahan, Min Dong, Q. Quinn Li, Chun Liang, Thomas J. Magliery and Christopher W. Bartlett. 2014. Addressing the unmet need for visualizing Conditional Random Fields in Biological Data. BMC Bioinformatics. 15: 202. Download paper

Zhixin Zhao, Xiaohui Wu, Praveen Kumar Raj Kumar, Min Dong, Guoli Ji, Q. Quinn Li* and Chun Liang*. 2014. Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms. Genes Genomics Genetics (G3). , 4(5):871-883. Download paper

Liuyin Ma, Pratap Kumar Pati, Man Liu, Q. Quinn Li* and Arthur G. Hunt*. 2014. High throughput characterizations of poly(A) site choice in plants. Methods, 67(1):74-83. Download paper

Liuyin Ma, Cheng Guo and Q Quinn Li*. 2014. Role of alternative polyadenylation in epigenetic silencing and antisilencing. Proc. Nat. Acad. Sci. USA, 111:9-10. Download paper

2013

Denghui Xing, Yajun Wang, Ruqiang Xu, Xinfu Ye, Dewei Yang, Q. Quinn 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.Download paper

Guoli Ji*, Yong Zeng, Jinting Guan, Q. Quinn Li, Congting Ye, Yunlong Liu. 2013. Recent advances in mathematical modeling and simulation of DNA replication process. Current Bioinformatics, 8:591-602. Download paper

2012

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

Arthur G. Hunt, Denghui Xing*, Q. Quinn Li*. 2012. Plant polyadenylation factors: conservation and variety. BMC Genomics, 13:641. Download paper

2011

Hongwei Zhao, Jun Zheng, Q. Quinn Li*. 2011. A novel plant in vitro assay system for pre-mRNA cleavage and polyadenylation. Plant Physiology, 157:1546-1554. Download paper

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

Xiaohui Wu, Man Liu, Bruce Downie, Chun Liang, Guoli Ji, Q. Quinn 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. Download paper

Jianti Zheng, Denghui Xing, Xiaohui Wu, Diana Kroll, Yingjia Shen, Guoli Ji*, Q. Quinn Li*. 2011. Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using Arabidopsis tiling microarray. PLoS One, 6:e14719. Download paper

2010

Denghui Xing, Q. Quinn Li*. 2010. Alternative polyadenylation and gene expression regulation in plants. WIREs (Willey Interdisciplinary Reviews) RNA, 2:445-458. (Invited review) Download paper

Guoli Ji*, Xiaohui Wu, Yingjia Shen, Jiangyin Huang, Zhoujing Wang and Q. Quinn Li. 2010. Classification-Based Prediction Models of Messenger RNA Polyadenylation Sites. Journal of Theoretical Biology, 265:287-296.Abstract

Guoli Ji*, Xiaohui Wu, Jiangyin Huang, Q. Quinn Li. 2010. Implementation of a Classification-Based Prediction Model for Plant mRNA Poly(A) Sites. Journal of Computational and Theoretical Nanoscience, 7(5):927-932.Abstract

2009

Hongwei Zhao, Denghui Xing, Q. Quinn Li*. 2009. Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies. Plant Physiology, 151:1546-1556.Download paper

Denghui Xing, Shuisong Ni, Michael A. Kennedy, Q. Quinn Li*. 2009. Identification of a plant-specific Zn-sensitive ribonuclease activity. Planta, 230:819-825. Download paper

Denghui Xing and Q. Quinn Li*. 2009. Alternative polyadenylation: a mechanism maximizing transcriptome diversity in higher eukaryotes. Plant Signaling and Behavior, 4:440-442. Download paper

2008

Denghui Xing, Hongwei Zhao and Q. Quinn Li *. 2008. Arabidopsis CLPS3, an ortholog of human polyadenylation factor CLP1, functions in gametophyte, embryo and post-embryonic development. Plant Physiology,148:2059-2069. Download paper

Denghui Xing, Hongwei Zhao, Ruqiang Xu and Q. Quinn Li* . 2008 . Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p, regulates FCA alternative processing and promotes flowering time. Plant Journal, 54:899-910. Download paper

Chun Liang*, Yuansheng Liu, Lin Liu, Adam C. Davis, Yingjia Shen, and Q. Quinn Li . 2008 ESTs with cDNA termini – previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii.   Genetics, 179:83-93 . Download paper

Yingjia Shen, Guoli Ji, Brian J. Haas, Xiaohui Wu, Jianti Zheng, Greg J. Reese, and Q. Quinn Li* . 2008 Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation.   Nucleic Acids Research, 36:3150-3161. Download paper

Yingjia Shen, Yuansheng Liu, Lin Liu, Chun Liang, and Q. Quinn 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). Download paper

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 Q. Quinn Li *. 2008 Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.   BMC Genomics, 9:220. Highly accessed at BMC Genomics webpage Download paper

Ruqiang Xu and Q. Quinn Li*. 2008. Streamline cloning of genes into binary vectors in Agrobacterium via the Gateway® TOPO vector system. Plant Methods, 4:4. Download paper

Jingxian Zhang, Kil-Young Yun , Ruqiang Xu, Arthur G. Hunt, Irina Artiushin, Kim Delaney, Q. Quinn Li and Deane L. Falcone*.   2008. Differential RNA processing implicated in responses of Arabidopsis thaliana to oxidative stress: a stress-tolerant mutant is deficient in a calmodulin-regulated RNA-binding protein. PLoS One , 3:e2410. Download paper

2007

Guoli Ji, Xiaohui Wu, Jianti Zheng, Yingjia Shen and Q. Quinn Li*. 2007. Modeling Plant mRNA Poly(A) sites: Software Design and Implementation. J. Computational Theoretical Nanoscience, 4:1365-1368.

Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, Ronghan Jiang, Yun Lin, Johnny C. Loke, Kimberly M. Davis, Greg J. Reese and Q. Quinn Li*.   2007.   Predictive modeling of plant messenger RNA polyadenylation sites.BMC Bioinformatics, 8:43 (doi:10.1186/1471-2105-8-43). Highly accessed at BMC Bioinformatics webpage Download paper

2006

Kim Delaney, Ruqiang Xu, Jingxian Zhang, Q. Quinn Li, Kil-Young Yun, Deane L. Falcone and Arthur G. Hunt*. 2006.   Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit.   Plant Physiology , 140:1507-1521.

Addepalli Balasubrahmanyam, Ruqiang Xu, Tomal Dattaroy, Baochun Li, W. Troy Bass, Q. Quinn Li and Arthur G. Hunt*. 2006. Disease resistance in plants that carry a feedback-regulated yeast poly(A) binding protein gene.  Plant Molecular Biology, 61:383 – 397.

Ruqiang Xu, Hongwei Zhao, Randy Dinkins, Xiaowen Cheng, George Carberry and Q. Quinn 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.

Hongyan Xing, Orlando Chambers, Chris B. Lawrence, H. Maelor Davies, Nicholas P. Everett and Q. Quinn Li *. 2006. Increased pathogen resistance and yield in transgenic plants expressing combinations of the modified antimicrobial peptides based on indolicidin and magainin.   Planta , 223:1024-1032.

 

Patents

Dave Francko, Ken Wilson, Q. Quinn Li, Alejandra Equiza. Plant Cryoprotectant Compositions and Methods of Use. US Patent 8580708 (Nov. 12, 2013). This patent has been used for commercial production. The product is under trademark Freezepruf.

Nicholas P. Everett, Q. Quinn Li , Christopher Lawrence, H. Maelor Davies. 2007. Peptides with enhanced stability to protease degradation. US Patent #7,214,766.

Quinn Li, Songhai Shen, Arthur G. Hunt and Shengyang He. 2002. Use of hrmA proteins and their genes for broad range protection of plants against bacterial, viral and fungal pathogens. US Patent #6342654

Arthur G. Hunt, Glen B. Collins, Q. Quinn Li, Christopher B. Lawrence and Santanu Dasgupta. 2002. Use of bacterial acetate kinase and their genes for protection of plants against different pathogens. US Patent # 6476293

Arthur G. Hunt, Q. Quinn Li, Jianjun Yang and Carol von Lanken. 2000. Use of yeast poly(A) binding proteins and their genes for broad range protection of plants against bacterial, fungal and viral pathogens. US Patent #6018106.