DECODING THE IMPACT OF TRANSPOSABLE ELEMENTS ON GENE REGULATION

至少一半的人类基因组来自转座元件(TES)。虽然有些人 研究认为TES是寄生的DNA，其他研究表明TES发挥着更具建设性的作用 通过为新的生物功能提供原料，在基因组进化中发挥作用。工商业污水附加费通常有活跃的顺位- 在进化过程中偶尔被增选的调控元件，以连接新的基因调控网络。 由于与以下方面相关的方法障碍，TES在高通量数据中仍未得到充分分析 它们的重复性。因此，TES对人类基因组调控的影响，在正常情况下 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TES在法规创新、保护和人类健康方面的影响的方法 疾病。在目标1中，我们结合了一种新的统计框架和大规模并行的报告基因分析 了解与基因调控有关的TE序列特征。我们将利用 TES的重复性将不同拷贝的TES中的序列变化与表观遗传学和功能性联系起来 差异，并使用新的基因组整合的大规模并行报告程序测试它们的调控活性 基因化验。在目标2中，我们将扩展目标1中开发的模型，以了解TES在 塑造基因组的3D拓扑，这与基因组功能密切相关。我们将量化 TES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，我们将开发技术来检测与疾病有关的TE基因融合。我们 目的检测表观基因去抑制的TES启动转录后拼接到下游的情况 基因，导致TE基因融合的嵌合RNA和蛋白质产物。我们将开发工具来检测这种情况 TE基因融合转录本，并将采用基于CRISPR的遗传和表观遗传工具，以便 操纵TES，这将使我们能够确定TES是否在这种类型的异常中起到因果作用 基因活性。在目标4中，我们将检验表观遗传抑制物通常用于治疗的假设 改变TES的表观遗传调控。通过这项提案的目标，我们希望加深对 什么序列特征驱动了TES的调节潜力，以及TES遵循的进化模式 调控网络进化过程中的不同TES家族。这样的理解将改善我们的情况 通过包括TES的影响来研究调节网络进化，TES是一类主要的快速进化序列，它 在功能基因组学研究中基本上被忽视了。本提案中开发的方法将具有 对ENCODE、Roadmap、TCGA等财团产生的数据的利用率产生很大影响 大型项目，目前从其数据中丢弃大多数TE派生序列。这样的改进 将反过来加速研究，以了解TES‘对正常基因调控和 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.