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

琴叶拟南芥和拟南芥的比较转座元件沉默和染色质分析

• 批准号: 197654083
• 负责人: Dr. Ales Pecinka
• 金额: --
• 依托单位: Institut für Genetik
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2011
• 资助国家: 德国
• 起止时间: 2010-12-31 至 2017-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/197654083?language=en
• 关键词: Comparative; transposable; element; silencing; chromatin

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.

转座因子（te）是植物基因组中高度动态的组成部分。在植物中，它们的活性通过嵌入转录抑制染色质而受到抑制。然而，一些先驱研究表明，这种控制可能在物种和压力条件下有所不同。拟南芥属的基因组资源使其成为探索这些现象在种间和进化背景下的程度的理想模型。我们以拟南芥和拟南芥为模型系统，对环境和温度变化条件下TE转位动力学、沉默模式和染色质组成进行了比较分析。在第一个资助期，我们制作了高通量测序样本，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，我们将重点关注以下目标：拟南芥和拟南芥种特异性TE激活分析。在这里，我们将利用全基因组转录组数据和我们的新分析方法来识别进化保守或多样化的TE沉默模式。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tes群体。拟南芥和拟南芥核小体景观的比较分析。我们生成了两个物种在环境温度、热量和恢复条件下的全基因组核小体和表达谱。接下来，我们将测试核小体在物种特异性、温度依赖性和转录依赖性方面的分布。这将大大增加我们对进化和胁迫过程中染色质变化的认识。非生物胁迫条件下野田鼠TE沉默的控制。我们确定了进化保守的和新的热应激反应te在A. lyrata和A. thaliana冷应激反应te。这将使我们能够寻找它们的共同特征，并测试与非生物应激条件相关的转位程度。总之，该项目将揭示在环境和应激条件下最大限度地减少TEs有害影响的物种特异性适应，以及在这场战斗中不完全从宿主基因组中消除TEs的对策。