Transposable element silencing in human somatic cells

 描述（由申请人提供）：为了更好地了解转座因子（TE）如何引起疾病，我们需要了解它们在人类细胞中是如何被控制的。在人类TE沉默途径中涉及的小RNA和蛋白质的知识方面存在空白。长期的目标是了解基因组是如何保护免受TE诱变的。本研究的目的是鉴定在TE生命周期的三个不同阶段中在TE沉默中起作用的小RNA和蛋白质。我们假设1）内源性siRNA和TE衍生的miRNA通过引导TE DNA甲基化和TE转录物降解在TE沉默中起作用;和2）体细胞突变负责TE去阻遏细胞中转座因子的激活。为了检验这些假设，我们将利用癌症样品作为TE去阻遏的模型。使用生物信息学，我们可以从癌症基因组图谱数据中提取TE衍生的小RNA、TE启动子的甲基化、TE转录水平和从头TE插入。利用这些TE上的变量，我们将鉴定参与TE沉默的小RNA和基因。对于目标1，我们将测试每个小RNA与TE去阻遏样品中甲基化和转录水平的显著相关性。对于目标2，我们将测试每个携带体细胞突变的基因座与去阻遏细胞中TE活性变化的关联。这种方法是创新的，因为它允许访问成千上万的自然实验与TE活动的变化。癌症-正常对的可用性允许全基因组关联研究方法，这在典型群体基因组数据之前是不可能的。这项工作的结果将是在人类体细胞中TE沉默中起作用的候选基因座的列表，以及人类TE沉默模型的全局图。这项研究意义重大，因为它将推进我们对人体细胞中TE沉默的分子细节的了解。这些知识将最终增加我们对TE引起的突变的理解，以及为什么TE在某些疾病中被去抑制。

 DESCRIPTION (provided by applicant): To better understand how transposable elements (TEs) cause disease, we need to understand how they are controlled in human cells. There is a gap in the knowledge of small RNAs and proteins involved in the TE silencing pathways in humans. The long- term goal is to understand how the genome is protected against the mutagenesis of TEs. The objective of this study is to identify small RNAs and proteins functioning in TE silencing in three separate stages of the TE life cycle. We hypothesize that 1) endogenous siRNAs and TE-derived miRNAs function in TE silencing by guiding TE DNA methylation and TE transcript degradation; and 2) somatic mutations are responsible for the activation of transposable elements in TE de-repressed cells. To test these hypotheses, we will utilize the cancer samples as the model for TE de-repression. Using bioinformatics, we can extract TE-derived small RNAs, methylation of TE promoters, TE transcript levels, and de-novo TE insertions from the Cancer Genome Atlas data. Using these variables on TEs, we will identify small RNAs and genes involved in TE silencing. For aim 1, we will test each small RNA for significant correlation with methylation and transcript levels across TE de-repressed samples. For aim 2, we will test each locus harboring somatic mutations for association with variation in TE activity in de-repressed cells. The approach is innovative, since it allows access to thousands of natural experiments with variation in TE activity. The availability of cancer-normal pairs allows a genome-wide associate study approach that was not possible before with typical population genomic data. The outcomes from this work will be a list of candidate loci that function in TE silencing in human somatic cells, and a global picture of the model for TE silencing in humans. The proposed research is significant because it will advance our knowledge on the molecular details of TE silencing in human somatic cells. This knowledge will ultimately increase our understanding of mutations caused by TEs, and why TEs are de-repressed in certain diseases.