Comparative transposable element silencing and chromatin analysis of Arabidopsis lyrata and Arabidopsis thaliana

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Transposable elements (TEs) are highly dynamic components of plant genomes. In plants, their activity is suppressed by embedding them into transcriptionally repressive chromatin. However, several pioneer studies indicated that this control may differ between species and under stress conditions.Genomic resources available for the Arabidopsis genus make it an ideal model for exploring the extent of these phenomena in the inter-specific and evolutionary context. We use Arabidopsis lyrata and Arabidopsis thaliana as the model system for comparative analysis of TE transposition dynamics, silencing patterns and chromatin makeup under ambient and temperature-shift conditions. In the first grant period, we produced high throughput sequencing samples, genome-wide annotation resources necessary for analyses, developed a novel method for analyzing TE expression and started the analyses. During the second funding period, we will focus on following objectives:1. Analysis of species-specific TE activation in A. lyrata and A. thaliana. Here, we will use the power of genome-wide transcriptome data and our novel analysis method to identify evolutionary conserved or diversified patterns of TE silencing. Our preliminary data indicate that, previously unanticipated, differential rules apply to specific groups of TEs.2. Comparative analysis of nucleosome landscape in A. lyrata and A. thaliana. We generated genome-wide nucleosome and expression profiles of both species under ambient temperature, heat and recovery conditions. Next, we will test for nucleosome distribution in species-specific, temperature-dependent and transcription-dependent manner. This will greatly increase our understanding on the chromatin changes in course of evolution and stress.3. Control of TE silencing under abiotic stress conditions in A. lyrata. We identified evolutionary conserved and novel heat stress-responsive TEs in A. lyrata and coldstress-responsive TEs in A. thaliana. This will allow us to search for their common characteristics and test for the extent of transposition linked to the abiotic stress conditions.In summary, this project will reveal species-specific adaptations for minimizing deleterious effects of TEs under ambient and stress conditions, as well as countermeasures of TEs not to be completely eliminated from the host genomes during this battle.