FLi

Research

Role of miRNA and tasiRNA genes in Resistance (R) gene regulation and evolution

Plant genomes contain a large number of closely related resistance (R)-genes whose encoded proteins recognize specific pathogen effectors and trigger resistance responses. The unregulated expression of R-genes can trigger autoimmunity in the absence of pathogen infection and severely inhibit plant growth. Despite this potentially serious effect on agricultural production, the mechanisms regulating R-gene expression are not well understood. Using a bioinformatics approach, we identified many conserved and Solanaceae specific miRNAs targeting a variety of functional R-genes and showed that many miRNAs cleave R-gene transcripts in vivo and trigger secondary siRNAs from cleaved transcripts. We further showed that R-gene targeting miRNAs are capable of regulate resistance in vivo. Analyses of the precusor sequences of these miRNAs revealed homology between the some miRNA precursors and corresponding R-gene targets, indicating part of these miRNA arise from insertion of R-gene fragments into the genome in a inverted-repeat manner. Our research indicated miRNAs play a broad role in R-gene regulation and evolution.

Role of gene associated transposable element (GATE) siRNA in gene regulation

Small RNAs, including tasiRNAs and miRNAs, play important role in development and response to environment. In most plant species, siRNA derived from transposable element (TE) constitutes the major population of endogenous small RNAs and play an essential role in restricting transposon activity. It is well known that many TEs, like MITE, SINE, and LTR, are gene associated (GATE). However, the role of GATE siRNA in nearby gene (gated gene) regulation is not very well investigated. Cultivated potato is a tetraploid plant propagated vegetatively which confers higher tolerance to TE insertion in or near genes and provides a good system to study GATE siRNA mediated gene regulation. In previous study we showed that GATE siRNA biogenesis requires RNA Dependent RNA Polymerase 2 (RDR2). In this project, we developed novel RNA sequencing approaches to experimentally annotate and quantify the expression level of potato gated genes, and investigated the effect of knocking-down  RDR2 on the accumulation of GATE siRNA and expression of corresponding gated genes. The goal is to investigate to which extent the GATE siRNA contribute to gated gene regulation.

Publication

Li F., Pignatta D., Bendix C., Brunkard J., Cohn M., Kumar P., Tung J., Sun H., and Baker B. 2011. 22-nt miRNAs regulate resistance (R)-genes and trigger R-gene secondary siRNA in Solanaceae. (submitted).

Li F., Orban R., and Baker B. 2011. SoMART, a webserver for plant miRNA, tasiRNA and target gene analysis in Solanaceae plants. (submitted)

Kuang H*, Padmanabhan C*, Li F.*, Kamei A, Bhaskar PB, Ouyang S, Jiang J, Buell CR, Baker B. 2009. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae. Genome Res 19, 42-56. (*Equal contribution)

Aliyari R, Wu Q, Li HW, Wang XH, Li F., Green LD, Han CS, Li WX, Ding SW. 2008. Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila. Cell Host Microbe. 4(4), 387-97.

Diaz-Pendon J.A., Li, F., Li, H.W., Li, W.X., and Ding, S.W. (2007) Suppression of Antiviral Silencing by Cucumber Mosaic virus 2b protein in Arabidopsis Is Associated with Drastically Reduced Accumulation of Three Classes of Viral siRNAs. Plant Cell, 19(6), 2053-63.

Li, F., and Ding, S.W. (2006) Virus Counterdefense: Diverse Strategies for Evading the RNA Silencing. Ann Rev. Microbiol. 60, 503-531.

Lu, R., Maduro, M., Li, F., Li, H.W., Broitman-Maduro, G., Li, W.X. and Ding, S.W. (2005) Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegans. Nature, 436, 1040-1043.

Khaled, A., Guo, S., Li, F. and Guo, P. (2005) Controllable self-assembly of nanoparticles for specific delivery of multiple therapeutic molecules to cancer cells using RNA nanotechnology.Nano Lett, 5, 1797-1808.

Ding, S.W., Li, H., Lu, R., Li, F. and Li, W.X. (2004) RNA silencing: a conserved antiviral immunity of plants and animals. Virus Res, 102, 109-115.

Li, W.X., Li, H., Lu, R., Li, F., Dus, M., Atkinson, P., Brydon, E.W., Johnson, K.L., Garcia-Sastre, A., Ball, L.A., Palese, P. and Ding, S.W. (2004) Interferon antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing. Proc Natl Acad Sci U S A, 101, 1350-1355.

Experience

2011 Jul-Present, Associate Specialist, UC Berkeley

2006 Oct-2011 Jun, Post-doctoral Researcher, UC Berkeley

2001 Sep-2006 Sep, Graduate Student Reseacher, UC Riverside

2000 Sep-2001 Jun, Undergraduate Student Researcher, Tsinghua University