DECODING THE IMPACT OF TRANSPOSABLE ELEMENTS ON GENE REGULATION

描述（由申请人提供）： 人类基因组中至少有一半来自转座因子（TE）。这些高度重复的元件通常具有转录因子结合位点和表观遗传调节信号。TE在进化过程中形成了基因调控网络，并且经常在疾病中失调。然而，TE序列在多大程度上对功能调控网络做出贡献，以及TE序列如何从寄生DNA进化为功能元件，仍然不清楚。这些问题的解决将扩大我们对调控网络的理解，包括TE对全基因组基因调控模式的贡献。在这个提议中，我们引入了一种新的策略，结合计算预测TE衍生的细胞类型特异性增强子与大规模并行报告基因检测，以了解TE对细胞类型特异性基因调控的影响。在具体目标1中，我们计划开发一种基于表观基因组学的方法来检测TE衍生的增强子及其靶基因。然后，我们将使用CRE-seq（一种大规模平行报告基因测定法）测试它们的调节活性。我们将使用计算模型来预测TE衍生的增强子。如果成功，我们不仅将产生最大的TE衍生细胞类型特异性增强子目录，而且我们将创建一个强大的框架，用于检测TE对任何细胞类型或组织中基因调控的贡献。在具体目标2中，我们将开发一种遗传学信息功能关联分析。我们将重建代表候选TE进化中间体的序列，并使用CRE-seq测试这些序列的调节活性。我们将解决的问题，包括是否特定类别的TE获得TF结合位点，然后迅速传播，或者是否TE首先传播，后来获得TF结合位点。如果成功的话，我们将了解什么样的序列特征驱动TE的功能潜力，以及在调控网络进化过程中不同TE家族所遵循的进化模式。这样的理解将通过纳入TE的影响来显着改善我们对基因调控网络进化的了解，TE是一类快速进化的调控序列，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对由诸如ENCODE、Roadmap Epigenomics、TCGA和其他大规模基因组学项目的联盟产生的数据的效用具有高度影响，这些联盟目前从其数据中丢弃大多数TE衍生序列。这种改进反过来将加速研究，以了解TE对正常基因调控和人类疾病的影响。

DESCRIPTION (provided by applicant): At least half of the human genome is derived from transposable elements (TEs). These highly repetitive elements often harbor transcription factor binding sites and epigenetic regulatory signals. TEs have shaped gene regulatory networks during evolution and are often dysregulated in diseases. However, the extent to which TEs contribute sequences to functional regulatory networks, and how TE sequences evolved from parasitic DNA to functional elements, remains unclear. Answering these questions will expand our understanding of regulatory networks by including the contributions of TEs to genome-wide patterns of gene regulation. In this proposal, we introduce a novel strategy that combines computational prediction of TE derived cell type-specific enhancers with massively parallel reporter gene assays to understand the impact of TEs to cell type-specific gene regulation. In Specific Aim 1 we plan to develop an epigenomics-based approach to detect TE-derived enhancers and their target genes. We will then test their regulatory activities using CRE-seq, a massive parallel reporter gene assay. We will bring to bear computational models that allow us to predict TE-derived enhancers. If successful, not only will we produce the largest catalog of TE-derived cell type-specific enhancers, but also we will have created a robust framework for detecting the contributions of TEs to gene regulation in any cell type or tissue. In Specific Aim 2 we will develop a phylogenetically informed functional association assay. We will reconstruct sequences representing the evolutionary intermediates of candidate TEs and test the regulatory activities of these sequences with CRE-seq. We will address questions including whether particular classes of TEs gained TF-binding sites and then spread quickly, or whether TEs first spread and later gained TF binding sites. If successful, we will develop an understanding of what sequence features drive the functional potential of TEs, and the modes of evolution followed by different families of TEs during regulatory network evolution. Such an understanding will dramatically improve our picture of gene regulatory network evolution by including the effects of TEs, a major class of fast evolving regulatory 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 Epigenomics, TCGA, and other large- scale genomics 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.