The food supply relies on plant crops. The production of most crops can be improved genetically, but this improvement requires a basic understanding of the functions of plant genes. The genes found most often in plants are called transposable elements, but surprisingly these genes usually do not fill a productive purpose. Instead, they are are the remnants of ancient invasions of the plant's DNA, probably by viruses. After invading, the viruses used the machinery of the plant to make copies of themselves and then their DNA remained permanently among the plant genes while retaining the ability make more copies of themselves. To counter the invasion and propagation of these elements, the plant tries to disable them, making them incapable of copying themselves. But it is not known how plants recognize transposable elements to disable them. Understanding this step is crucial for understanding the history and function of plant genes, and it may also inform processes used for genetically engineering crops. This award focuses on understanding how a plant recognizes transposable elements to disable them. The award will also train postdoctoral and graduate students in the methods and computational tools used to study plant genes creating a broader societal impact.
Interactions between a plant and its transposable elements represent an ongoing conflict. Elements seek to propagate while plants try to control their propagation through epigenetic silencing. An important component of the epigenetic response is small RNAs, which guide the plant's silencing machinery to their genomic targets by sequence similarity. Because of this similarity, the mapping locations of small RNAs provide insights about their putative targets and also about the loci from which they may have originated. It is not known, however, how the initial small RNAs are generated. Previous work has shown that small RNAs in maize (Zea mays) map preferentially to regions of the element that form secondary structures. The regions that are particularly prone to folding in our study system (Sirevirus elements) are also necessary for their function. It is hypothesized that folding regions of transposable elements are processed directly into small RNAs, thereby initiating the host silencing response. These folding regions are predicted to be important for the initiation of the host response and also to be the focus of an evolutionary arms race between plants and their hosts. The first prediction will be tested by inserting folding regions from maize Sirevirus elements into Arabidopsis thaliana transgenically, to see if these regions are sufficient to initiate a plant response. The latter prediction will be examined by studying small RNAs and Sirevirus elements in several different plants, including maize and other grain crops. If the folding regions are the locus of host-element interactions, then small RNAs should preferentially map to these regions.