Plant Pathology Graduate Program

Shou-Wei Ding

Shou-Wei Ding
Office: 951-827-2341
3202A Genomics
Office Hours: , not specified - not specified
Email: dingsw@ucr.edu

Shou-Wei Ding

Professor: Molecular Virology and Immunology

PhD -- Australian National University (Canberra, Australia)

Participating Graduate programs: (i) Cell, Molecular & Developmental Biology; (ii) Genetics, Genomics & Bioinformatics; (iii) Microbiology; (iv) Plant Pathology

Biography & Research Interests

My research programs focus on the host immune responses to RNA viruses and viral counter-defense strategies. Viruses with an RNA genome exhibit distinct genetic and immunological properties from DNA viruses. > 70% of plant viruses are RNA viruses and many important human diseases (e.g. influenza, avian influenza, SARS, Ebola, Dengue, West Nile and polio) are caused by RNA viruses. RNA viruses that infect plants, invertebrates and vertebrates are remarkably similar in genome structure and replication strategies. Recent studies suggest that eukaryotic hosts have evolved a conserved mechanism to direct antiviral defense across the kingdoms.

We have been taking a comparative approach to identify and characterize antiviral immunity mechanisms in plants and animals. Genetic models have been developed in Drosophila melanogaster, Arabidopsis thaliana and Caenorhabditis elegans to investigate the molecular interactions of RNA viruses with their hosts. Studies from my lab and others have shown that RNA viruses are targeted in both plants and invertebrates by a form of antiviral immunity that confers virus resistance by RNA interference (RNAi). In antiviral RNAi, viral dsRNA replicative intermediates are processed by the RNaseIII Dicer into siRNAs, which guide specific silencing of complementary viral RNAs by RNaseH-like Argonaute proteins. As a result, successful virus infection in plants and invertebrates requires suppression of the antiviral immunity by a distinct class of viral proteins known as viral suppressors of RNAi (VSRs). Our recent studies show that RNAi also directs antiviral immunity in a mouse model based on the infection by Nodamura virus, which is closely related to Flock house virus used extensively in our previous studies in Drosophila.

Current projects in the lab aim to identify new components in antiviral immunity pathways by unbiased forward genetic screens and to determine if RNAi is also antiviral against human RNA viruses.


Fellow, American Association for the Advancement of Science, 2006

Fellow, American Academy of Microbiology, 2012


Selected Research Articles

Ding SW and Voinnet O. 2014. Antiviral RNA silencing is mammals: No news is not good news. Cell Rep 9: 795-797.

Zhang Z, Qi S, Tang N, Zhang X, Chen S, Zhu P, Ma L, Cheng J, Xu Y, Lu M, Wang H, Ding SW, Li S, and Wu Q. (2014) Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms. PLoS Pathog 10(12): e1004553. doi:10.1371/journal.ppat.1004553

Cao MJ, Du P, Wang XB, Yu YQ, Qiu YH, Li WX, Gal-On A, Zhou CY, Li Y, Ding SW. 2014. Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis. Proc Natl Acad Sci USA 111(40): 14613-8.

Gaulke C, Porter M, Han YH, Sankaran-Walters S, Grishina I, George M, Dang A, Ding SW, Jiang G, Korf I, Dandekar S 2014. Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and simian immunodeficiency virus infections. J Virol 88:6268–6280

Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: A fast and accurate adapter trimmer for Next-Generation Sequencing (NGS) paired-end reads. BMC Bioinformatics 15:182. doi:10.1186/1471-2105-15-182

Guo X, Zhang R, Wang J, Ding SW, Lu R. 2013. Homologous RIG-I-like helicase proteins direct RNAi-mediated antiviral immunity in C. elegans by distinct mechanisms. Proc Natl Acad Sci USA. 110:16085-90

Maillard PV, Ciaudo C, Marchais A, Li Y, Jay F, Ding SW, Voinnet O. Antiviral RNA interference in mammalian cells. Science 342:235-238 (Li Y is a postdoc in my lab).

Li Y, Lu JF, Han YH, Fan XX and Ding SW. 2013. RNA interference functions as an antiviral immunity mechanism in mammals. Science 342:231-234

Wu Q, Wang Y, Cao MJ, Pantaleo V, Burgyan J, Li WX and Ding SW. 2012. Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci USA 109:3938-3943.

Duan CG, Fang YY, Zhou BJ, Zhao JH, Hou WN, Zhu H, Ding SW, Guo HS. 2012. Suppression of Arabidopsis ARGONAUTE1-mediated slicing, transgene-induced RNA silencing, and DNA methylation by distinct domains of the cucumber mosaic virus 2b protein. Plant Cell 24:259-274.

Han YH, Luo YJ, Wu Q, Jovel J, Wang XH, Aliyari R, Han C, Li WX and Ding SW. 2011. RNA-based immunity terminates viral infection in adult Drosophila in absence of viral suppression of RNAi: Characterization of viral siRNA populations in wildtype and mutant flies. J Virol 85(24):13153-63.

Wang XB, Jovel J, Udomporn P, Wang Y, Wu Q, Li WX, Gasciolli V, Vaucheret H and Ding SW. 2011. The 21-nucleotide, but not 22-nucleotide, viral secondary small interfering RNAs direct potent antiviral defense by two cooperative Argonautes in Arabidopsis thaliana. Plant Cell 23:1625-38.

Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX, and Ding SW. 2010. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci USA. 107, 1606-1611.

Wang XB, Wu Q, Ito T, Cillo F, Li WX, Chen X, Yu JL, and Ding SW. 2010. RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci USA 107, 484-489.

Lu R, Yigit E, Li WX and Ding SW. 2009. An RIG-I-like RNA helicase mediates antiviral RNAi downstream of viral siRNA biogenesis in Caenorhabditis elegans. PloS Pathogens 5(2):e1000286

Aliyari R, Wu QF, L HW, Wang XH, Li F, Green LD Han CS, Li WX, and Ding SW. 2008. Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in DrosophilaCell Host & Microbe 4:387-397

Diaz-Pendon JA, Li F, Li WX, Ding SW. 2007. Suppression of antiviral silencing by cucumber mosaic virus 2b protein inArabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell 19:2053-63.

Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P, and Ding SW. 2006. RNA interference directs innate immunity against viruses in adult  Drosophila. Science 312:452-4

Lu R, Maduro M, Li F, Li HW, Maduro G, Li WX and Ding SW. 2005. Animal virus replication and RNAi-mediated antiviralin Caenorhabditis  elegans.Nature 436:1040-1043.

Chen J, Li WX, Xie DX, Peng JR & Ding SW. 2004. Viral virulence protein suppresses RNA silencing-mediated defense but upregulates the role of miRNA in host gene expression. Plant Cell 16:1302-1313.

Lu R, Folimonov A, Shintaku M, Li WX, Falk BW, Dawson WO, and Ding SW. 2004. Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome. Proc Natl Acad Sci USA101:15742-15747.

Li WX, Li HW, Lu R, Li F, Dus M, Atkinson P, Johnson KL, Garcia-Sastre A, Brydon E, Ball LA, Palese P & Ding SW. (2004) Interferon antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing. Proc Natl Acad Sci USA101:1350-1355.

Li HW, Li WX, & Ding SW. 2002. Induction and suppression of RNA silencing by an animal virus. Science 296, 1319-1321.

Guo HS & Ding SW. 2002. A viral protein inhibits the long-range signaling activity of the gene silencing signal. EMBO J21, 398-407.

Ji LH & Ding SW. 2001. The suppressor of transgene RNA silencing encoded by cucumber mosaic virus interferes with salicylic acid-mediated virus resistance. Mol Plant-Microbe Interact 14, 715-724.

Lucy AP, Guo HS, Li WX, & Ding SW.  2000. Suppression of post-transcriptional gene silencing by a plant viral protein localised in the nucleus. EMBO J 19, 1672-1680

Li HW, Lucy AP, Guo HS, Li WX, Ji LH, Wong SM, & Ding SW. 1999. Strong host resistance targeted against a viral suppressor of the plant gene silencing defence mechanism. EMBO J 18, 2683-2691

Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW & Baulcombe DC. 1998. Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J 17, 6739-6746.


Selected Review Articles

Ding SW and Lu R. 2011. Virus-derived siRNAs and piRNAs in immunity and pathogenesis. Curr Opin Virol 1, 533-544

Ding SW. RNA-based antiviral immunity. 2010. Nature Rev Immunol 10:632-44 (on the cover)

Wu QF, Wang XB and Ding SW. 2010. Viral suppressors of RNA-based viral immunity: Host targets. Cell Host & Microbe 8:12-15.

Aliyari R, and Ding SW. 2009. RNA-based viral immunity initiated by the Dicer family of host immune receptors. Immunol Rev 227: 176-188

Diaz-Pendon JA and Ding SW. 2008. Direct and indirect roles of viral suppressors of RNA silencing in pathogenesis. Ann Rev Phytopath 46:303-326

Ding SW, and Voinnet O. 2007. Antiviral immunity directed by small RNAs. Cell 130, 413-426

Li F, and Ding SW. 2006. Virus counterdefense: Diverse strategies for evading the RNA silencing immunity. Ann Rev Microbiol 60:503-531.

Li HW, and Ding SW. 2005. Antiviral silencing in animals. FEBS Lett 579, 5965-5973

Ding SW, Li HW, Lu R, Li F and Li WX. 2004. RNA silencing: A conserved antiviral immunity of plants and animals. Virus Res 102, 109-115.

Mlotswa S, Voinnet O, Mette F, Matzke M, Vaucheret H, Ding SW, Pruss G, and Vance VB. 2002. RNA silencing and the mobile silencing signal. Plant Cell S289-S301.

Li WX and Ding SW. 2001. Viral suppressors of RNA silencing. Curr Opin Biotechnol 12, 150-154

Ding SW. RNA silencing. 2000. Curr Opin Biotechnol 11, 152-156.

More Information

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