DECODING THE IMPACT OF TRANSPOSABLE ELEMENTS ON GENE REGULATION

人类基因组中至少有一半来自转座因子（TE）。虽然一些 一些研究认为TEs是“寄生的”DNA，其他研究则认为TEs起着更积极的作用 通过提供新生物功能的原材料来促进基因组进化。TE通常具有活性顺式- 在进化过程中偶尔被选择的调控元件连接新的基因调控网络。 在高通量数据中，由于与以下因素相关的方法学障碍， 重复的性质。因此，TE对人类基因组调控的影响，无论是在正常的 发展和疾病，在很大程度上仍然没有特征。我们建议发展先进的基因组学 评估和澄清技术教育对监管创新、保护和人类健康的影响的方法 疾病在目标1中，我们将联合收割机与大规模并行报告基因检测结合起来 了解有助于基因调控的TE序列特征。我们将利用 TE的重复性质将TE的不同拷贝中的序列变化与表观遗传和功能 差异，并使用一种新的基因组整合的大规模平行报告测试其调节活性 基因检测在目标2中，我们将扩展目标1中开发的模型，以了解TE在以下方面的作用： 塑造基因组的3D拓扑结构，这与基因组功能密切相关。我们将量化 TE在多大程度上构成了基因组拓扑结构的保守性和/或差异性， 哺乳动物物种。在目标3中，我们将开发检测与疾病相关的TE基因融合的技术。我们 目的是检测表观遗传去抑制的TE启动转录本剪接成下游的情况， 基因，产生TE-基因融合嵌合RNA和蛋白质产物。我们将开发工具来检测这种 TE基因融合转录物，并将采用基于CRISPR的遗传和表观遗传工具， 操纵TE，这将使我们能够确定TE是否在这种类型的异常中发挥因果作用。 基因活性在目标4中，我们将检验通常用于治疗的表观遗传抑制剂的假设， 改变TE的表观遗传调节。我们希望通过本提案的目的， 什么样的序列特征驱动TE的调节潜力，以及随后的进化模式， 在监管网络演进过程中的不同TE家族。这样的理解将改善我们的画面 调节网络的演变，包括TE的影响，一个主要类别的快速演变的序列， 在功能基因组学研究中被忽视了。本提案中开发的方法将具有 对ENCODE、Roadmap、TCGA等联盟产生的数据的实用性有很大影响， 大规模的项目，目前从他们的数据中丢弃大多数TE衍生序列。这种改善 反过来，这将加速研究了解TE对正常基因调控的影响， 人类疾病。

At least half of the human genome is derived from transposable elements (TEs). While some investigations regard TEs as “parasitic” DNA, other studies suggest that TEs play a more constructive role in genome evolution by providing raw material for new biological functions. TEs commonly harbor active cis- regulatory elements that are occasionally co-opted during evolution to wire new gene regulatory networks. TEs remain under-analyzed in high-throughput data because of methodological hurdles associated with their repetitive nature. Thus, the impact of TEs on the regulation of the human genome, both in normal development and disease, remains largely uncharacterized. We propose to develop advanced genomics approaches to assess and clarify the impact of TEs in regulatory innovation, conservation, and in human diseases. In Aim 1 we combine a novel statistical framework with massively parallel reporter gene assays to understand TE sequence features that contribute to gene regulation. We will take advantage of the repetitive nature of TEs to link sequence changes in different copies of TEs to epigenetic and functional differences, and test their regulatory activities using a new genome integrated massive parallel reporter gene assay. In Aim 2 we will extend the models developed in Aim 1 to understand the role of TEs in shaping the 3D topology of the genome, which is intimately connected to genome function. We will quantify the extent to which TEs underlie the conservation and/or divergence of genome topology across mammalian species. In Aim 3 we will develop technologies to detect TE-gene fusions linked to disease. We aim to detect cases where epigenetically de-repressed TEs initiate transcripts that splice into downstream genes, resulting in TE-gene fusion chimeric RNA and protein products. We will develop tools to detect such TE-gene fusion transcripts, and will adapt CRISPR-based genetic and epigenetic tools in order to manipulate TEs, which will allow us to establish whether TEs play a causal role in this type of abnormal gene activity. In Aim 4 we will test the hypothesis that epigenetic inhibitors commonly used for therapeutics alter TEs’ epigenetic regulation. Through the aims of this proposal we hope to develop an understanding of what sequence features drive the regulatory potential of TEs, and the modes of evolution followed by different families of TEs during regulatory network evolution. Such an understanding will improve our picture of regulatory network evolution by including the effects of TEs, a major class of fast evolving sequences that have been largely ignored in functional genomics studies. The methods developed in this proposal will have a high impact on the utility of data produced by consortia such as ENCODE, Roadmap, TCGA, and other large-scale projects, which currently discard most TE derived sequences from their data. Such improvement will in turn accelerate research into understanding the impact of TEs’ on normal gene regulation and in human diseases.