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

转座元件(TES)是植物基因组中高度动态的组成部分。在植物中，它们的活性通过将它们嵌入转录抑制的染色质而受到抑制。然而，一些开创性的研究表明，这种控制可能在物种和胁迫条件下有所不同。拟南芥属的基因组资源使其成为在种间和进化背景下探索这些现象程度的理想模型。我们以拟南芥和拟南芥为模型系统，比较分析了环境和温度变化条件下的TE转座动态、沉默模式和染色质组成。在第一次资助期间，我们制作了高通量测序样本，这是分析所需的全基因组注释资源，开发了一种分析TE表达的新方法，并开始了分析。在第二个资助期内，我们将专注于以下目标：1.分析柳杉和柳杉中特定物种的TE激活。在这里，我们将使用全基因组转录组数据的力量和我们的新分析方法来识别TE沉默的进化保守或多样化模式。我们的初步数据表明，以前没有预料到的是，不同的规则适用于特定的TE组。柳杉和柳杉核小体景观的比较分析。我们生成了两个物种在环境温度、高温和恢复条件下的全基因组核小体和表达谱。接下来，我们将以物种特异性、温度依赖和转录依赖的方式测试核小体分布。这将大大增加我们对染色质在进化和应激过程中变化的理解。非生物胁迫条件下赖草TE沉默的调控。我们在羊栖菜中发现了进化保守的和新的热应激响应的TES，在海桑中发现了冷应激响应的TES。这将使我们能够寻找它们的共同特征，并测试与非生物胁迫条件相关的转位程度。综上所述，本项目将揭示在环境和胁迫条件下将TES的有害影响降至最低的物种特有的适应，以及在这场战斗中不完全从寄主基因组中消除TES的对策。

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.