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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.
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.
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