Dynamic regulatory impact of human transposable elements on gene expression

摘要 多达50%的灵长类基因组由转座元件(TES)组成。而这些元素 最初被认为是垃圾DNA，新的技术和方法提供了对TES如何 可以对分子和生物表型做出贡献。考虑到他们当前或以前的能力在 寄主基因组，TES有可能通过以下方式对生物体产生有益和有害的影响 贡献基因调控序列。事实上，TES可以产生基因监管创新，从而导致 进化的新颖性和适应性，而TE错误的调节与包括癌症在内的各种疾病有关。 尽管TES很普遍，但我们对人类体内数百万种这些成分的了解相对较少 基因组对基因组的功能和表达起着重要作用。我们最重要的假设是TES发挥了他们的基因 在特定环境背景下的监管效果。为了开始剖析人类的TE规则，这项提案将 在人类个体细胞培养模型中利用进化功能基因组学方法 和我们进化上最接近的近亲黑猩猩。为了支持我们的假设，我们之前的工作，一起 已经表明TES确实可以通过染色质修饰、DNA 甲基化和转录因子结合。我们还表明，基因表达是动态响应的。 对物种内和物种之间的环境的影响，这支持了非编码基因组在调节 通过基因调控的表型效应。我们利用了一种灵活的诱导多能干细胞 基于(IPSC)的系统，以产生可仔细干扰的细胞类型，允许基因调控和 细胞反应有待确定和关联。在本提案中，我们将使用IPSC技术应用于 人类和黑猩猩个体组成的小组，以及功能基因组学和细胞分析 转座元件在调节表型效应中的作用。首先，我们将对TE监管进行调查 通过问：1)TES如何对灵长类动物的细胞类型规范做出贡献？ 2)TES如何影响灵长类动物的生殖层规格？第二，我们将研究进化 通过问3)应激反应是如何演变的 灵长类动物？4)TES对灵长类动物的压力反应有贡献吗？我们的研究将导致一种理解 TES作为基因组中可能仅在特定细胞中揭示的调节序列的可能性 国家，或对扰动的反应。这最终可能提供对异常监管的洞察，并通过 TES可能会导致疾病状态。

SUMMARY As much as 50% of primate genomes are comprised of transposable elements (TEs). While these elements were originally thought to be junk DNA, newer technologies and approaches have provided insight into how TEs can contribute to molecular and organismal phenotypes. Given their current or previous ability to move within host genomes, TEs have the potential to exert both beneficial and deleterious effects on the organism by contributing gene regulatory sequence. Indeed, TEs can generate gene regulatory innovation leading to evolutionary novelty and adaptation, while TE mis-regulation associates with various diseases including cancer. Despite the prevalence of TEs we understand relatively little about how millions of these elements in the human genome contribute to genome function and expression. Our overarching hypothesis is that TEs exert their gene regulatory effects in specific environmental contexts. To begin to dissect human TE regulation, this proposal will make use of evolutionary functional genomics approaches in a cell culture model derived from human individuals and our closest evolutionary relatives the chimpanzee. In support of our hypothesis, our previous work, together with that of many others, has indicated that TEs can indeed be regulated through chromatin modifications, DNA methylation and transcription factor binding. We have also shown that gene expression is dynamic in response to the environment within and between species, which supports the role of the non-coding genome in mediating phenotypic effects through gene regulation. We have taken advantage of a flexible induced pluripotent stem cell (iPSC) based system to generate cell types that can be carefully perturbed, allowing for gene regulatory and cellular responses to be determined and correlated. In this proposal we will use iPSC technology applied to a panel of human and chimpanzee individuals, together with functional genomics and cellular assays to dissect the role of transposable elements in mediating phenotypic effects. First, we will investigate TE regulatory dynamics during lineage commitment by asking: 1) How do TEs contribute to cell type specification in primates? and 2) How do TEs contribute to germ layer specification in primates? Second, we will investigate the evolution of TE regulatory dynamics in response to cellular stress by asking 3) How do stress responses evolve in primates? and 4) Do TEs contribute to stress responses in primates? Our research will result in an understanding of the potential for TEs to act as regulatory sequence in the genome that may only be revealed in particular cell states, or in response to perturbation. This may ultimately provide insight into how aberrant regulation of, and by TEs can contribute to disease states.