Transposable elements are DNA fragments in a genome that can mobilize and create mutations by inserting into new locations. To guard against this mutagenic outcome, cells have evolved mechanisms to interfere with transposable element mobilization. Previous work established a role for small RNAs in transposable element inhibition. This project will use modern genomics-enabled approaches in the model plant, Arabidopsis thaliana, to conduct a 'severe test' of the assumptions and conclusions that led to the prevailing mechanistic view and to expand understanding of how transposable element silencing is triggered. Because transposable elements are widespread in the genomes of both plants and animals, the results are expected to have broad impact in the field of regulatory biology. The project will also have strong educational impact, as it emphasizes data reproducibility and scientific ethics in three contexts: curricular enrichment for undergraduates who will integrate the research in their laboratory courses; annual outreach workshops for 7th grade minority students focused on science, technology, engineering and mathematics; and direct participation in research by early-career scientists at postdoctoral, graduate, and undergraduate levels.
The mobility and mutagenic potential of transposable elements depends on mRNAs produced by synthesis of RNAs (transcription) from the elements themselves. This transcription step is a key control point for regulating transposable element mobility. Previous work has shown that transcription of transposable elements is turned off by small RNAs, which initiate silencing by a post-transcriptional interference mechanism that transitions to transcriptional-level silencing. This project will reproduce key aspects of that previous work and will apply modern technological capabilities to produce higher-value datasets that will be analyzed in creative and innovative ways to determine precisely how RNA interference is targeted to a particular transcript and how RNA-directed DNA methylation and transcriptional-level repression are established to produce trans-generational epigenetic silencing of transposable elements. Data and protocols will be broadly disseminated via open-access routes to enable the reproducibility of the research. The results should provide not only new understanding of how RNA-mediated silencing occurs, but also clues about how such silencing could be prevented. These insights could have practical consequences for genetically engineering plants with agronomic benefit.
