Expression and Impact of Interspersed Repeats

摘要 内源性逆转录病毒和相关的转座元件构成了我们基因组的大部分，以及活性形式 作为长时间散布的Element-1(Line-1，L1)反转录转座子和它动员的Element-1持续存在。这些是 通过RNA中间体的反转录进行自我复制的自我传播序列。 我们已经开发出复杂的机制来抑制它们的转录并限制它们的增殖。然而，a 仔细的RNAseq分析表明，单个转座子基因座(ITL)的子集逃逸 沉默并在转录上活跃。在一项对正常人类细胞的调查中，我们发现了构成细胞和 可变表达的ITL。我们测量这些成绩单的能力提供了一个独特的机会来研究这一点 寄主-病原菌关系及其在基因调控中的作用。在这里，我们建议检验以下假设 逆转录元件的表达(或缺乏)是顺式作用的特定调控机制的指标 对邻近基因的影响。我们建议定义人类中表达的反转录转座子的图景； 演示转录沉默和逃逸的分子机制，并探索这些机制是如何 影响人类“表观遗传”疾病的基因表达。我们将使用基因组编辑策略来测试 改变ITL序列会影响邻近基因的表达。最后，我们将开发研究方法 流行的、高表达的短散布元件(Sine)，以评估其潜在的 逆转录转座，确定它们是RNA编辑的目标还是dsRNA传感通路的目标，并测试 它们与细胞内反式核糖核酸的相互作用。这些研究将是第一批深入研究 反转录转座子中间产物在人类细胞中的广泛表达和功能。

Summary Endogenous retroviruses and related transposable elements make up much of our genome, and active forms persist as long interspersed element-1 (LINE-1, L1) retrotransposons and the elements it mobilizes. These are self-propagating sequences which copy themselves through the reverse transcription of RNA intermediates. We have developed elaborate mechanisms to silence their transcription and limit their proliferation. However, a careful approach to RNAseq analysis reveals that that a subset of individual transposon loci (ITL) escape silencing and are transcriptionally active. In a survey of normal human cells, we identify both constitutive and variably expressed ITL. Our ability to measure these transcripts provides a unique opportunity to examine this host-pathogen relationship and its role in gene regulation. Here, we propose to test the hypothesis that retroelement expression (or lack thereof) is an indicator of specific regulatory mechanisms with cis-acting effects on neighboring genes. We propose to define the landscape of expressed retrotransposons in humans; demonstrate molecular mechanisms of transcriptional silencing and escape; and probe how these mechanisms affect gene expression in human ‘epigenetic’ diseases. We will use genome editing strategies to test whether altering ITL sequences affects neighboring gene expression. Finally, we will develop approaches to study prevalent, highly-expressed short interspersed elements (SINEs) to assess their potential for retrotransposition, determine whether they are targets of RNA editing or dsRNA sensing pathways, and test their interactions with cellular mRNAs in trans. These studies will be among the first to delve into the expression and function of a broad range of retrotransposon intermediates in human cells.