Genetic and molecular analysis of chromosomal determinants of transposon silencing in euchromatin

真核生物基因组中含有很大比例的转座元件(TE)和重复序列。通过它们的动员和转座，这些序列具有很高的诱变潜力。这威胁到基因组的完整性，但也为选择提供了一个重要的遗传变异来源。因此，生物体已经进化出限制TE活动的机制。在理解TE沉默的机制方面已经取得了很大进展。然而，TE与宿主染色质相互作用的许多方面仍然没有解决。特别是，目前尚不清楚基因如何限制/影响附近TE的沉默。我们以前已经发现，插入到蛋白质编码基因3(质数)端的TE可以逃脱沉默，并且在A.thaliana谱系中，单个TE的沉默存在相当大的差异。这些插入在进化水平上是稳定的，不会干扰TE或蛋白质基因的转录。基于这些发现，我们将集中在两个关键问题上：1)插入基因3(质数)端与逃避沉默之间的相关性有多普遍？2)这种逃避沉默的机制基础是什么？为了研究这些问题，我们将从生物信息学的角度分析3(质点)末端插入和沉默丧失之间的相关性在种群水平上有多广泛。我们将通过测试核小体重塑、3(质数)末端处理和抗沉默因子的参与来进一步研究这种沉默逃脱的机制基础。申请者之前已经确定了一个这样的反沉默因素。我们将把这与实验室中生成的新生成的TE插入的行为相关联。总之，这项工作将为以下重要问题提供见解：转座子沉默是如何在常染背景下启动和维持的，以及TE和宿主基因是如何相互影响的。此外，这项工作将为3(质数)末端的形成和转录终止的调节提供洞察力。因此，这项研究将有助于我们理解基因组的组织和调控。

Eukaryotic genomes contain a large proportion of transposable elements (TE) and repetitive sequences. Through their mobilization and transposition, these sequences have a high mutagenic potential. This threatens genome integrity but also provides an important source of genetic variation for selection to act upon. Thus, organisms have evolved mechanisms to limit TE activity. Much progress towards an understanding of mechanisms underlying TE silencing has been made. However, many aspects of TE interaction with the host chromatin remain unresolved. In particular, it remains unknown how genes limit/affect the silencing of nearby TE. We have previously found that TE inserted into the 3(prime) end of protein-coding genes escape silencing and that there is considerable variation in the silencing of individual TEs in the A. thaliana lineage. These insertions are stable at the evolutionary scale and do not interfere with transcription of the TE or the protein gene. Based on these findings, we will focus on two key questions: 1) How widespread is the correlation between insertion into the 3(prime) end of genes and escape from silencing? 2) What is the mechanistic basis of this escape from silencing? To investigate these questions, we will bioinformatically analyze how widespread the correlation between 3(prime) end insertion and loss of silencing is at the population level. We will further investigate the mechanistic basis of this escape from silencing by testing the involvement of nucleosome remodeling, 3(prime) end processing and anti-silencing factors. One such anti-silencing factor has been previously identified by the applicants. We will correlate this with the behavior of newly generated TE insertions generated in the lab. Together, this work will provide insights into the important question of how transposon silencing is initiated and maintained in a euchromatic context, as well as how TE and host genes reciprocally influence each other. In addition, this work will provide insight into the regulation of 3(prime) end formation and termination of transcription. Thus, this study will contribute to our understanding of genome organization and regulation.