Mechanisms of gene regulation mediated by human-specific SVA transposons

摘要 转座元件(TES)约占人类基因组的50%，现在有几条证据表明 这表明这些寄生成分作为哺乳动物基因调控新颖性的关键来源具有广泛的作用。 在此背景下，我的实验室旨在揭示TES用来调节和重新连接哺乳动物的机制 基因调控网络。特别是，我们致力于解决的根本问题是如何在最近 年轻的可移动元件(Sine-VNTR-Alus=Svas)的基因组入侵为人类特有的 特征。在5个主要的TE纲中，SVA是最年轻的，包括7个亚科，要么是原始人，要么是 特定的(SVA-A、-B、-C和-D)或人类特定的(SVA-E、-F和F1)。重要的是，SVA仍然是复制的 在人类中是有能力的，超过60%的现有人类SVA拷贝位于编码的10kb以内 吉恩。考虑到它们的年龄很小，SGA对于理解人类进化特别相关。我们的预赛 数据显示，人类特异性SVA插入体附近的基因在生物过程中得到了丰富 与大脑发育、头面部形态和认知行为有关。此外，SVA是 在众多基因中最表观的去抑制和转录上调的TE中 癌症。我们最近的工作表明，绝大多数人类特有的增强子和启动子 包含SVA插入，且增强子体内SVA转座与增加或 相关基因表达减少，具有明确的组织特异性模式。尽管有显眼的 一系列证据表明SVA是人类基因表达的重要调控者，我们仍然有限 了解这些TES的生物学知识。例如，我们不知道SVA通过什么机制增强 并抑制宿主基因、组织--尤其是组织--的转录活性。我们不知道是哪个成分(S) 这些TES的模块化结构推动了监管活动。最后，也是更重要的是，我们不知道 人类特有的SVA对人类特有的调控网络的重新布线的相对贡献，以及 人类特有特征的产生。为了填补这些知识空白，我们将把我们的基因组专业知识应用于 人和黑猩猩以海马神经发生为基础诱导多能干细胞分化 原则性证明。此外，为了解决这一机制，我们将利用人类细胞系CRISPR/Cas9和 基因组学。我们将解构Svas复杂的模块化体系结构，并定义所采用的机制 由SGA驱动宿主基因组上的调节活动。我们将深入研究组织特异性抑制活动 由选定的SVA显示以揭示潜在机制，还测试了以下假设 SVAs为关键的转录抑制因子(YY1)提供全基因组底物。与拟议的研究 我们将获得关于人类特有特征是如何产生的变革性见解，并将阐明为什么 SVAs的失调在包括癌症和神经疾病在内的疾病中经常被观察到。

Summary Transposable Elements (TEs) account for ~50% of the human genome, and several lines of evidence now suggest an extensive role for these parasitic elements as a critical source of gene-regulatory novelty in mammals. In this context, my laboratory aims at unveiling the mechanisms that TEs adopt to regulate and rewire mammalian gene regulatory networks. In particular, the fundamental problem that we aim to solve is how a very recent genomic invasion by young mobile elements (SINE-VNTR-Alus = SVAs) has set the ground for human-specific traits. Among the 5 main TE classes, SVAs are the youngest, and include 7 subfamilies being either hominid- specific (SVA-A, -B, -C, and -D) or human-specific (SVA-E, -F, and F1). Importantly, SVAs are still replication competent in humans, and over 60% of the existing human SVA copies are located within 10 kb of a coding gene. Given their young age, SVAs are particularly relevant for understanding human evolution. Our preliminary data show that genes proximal to human-specific SVA insertions are enriched for biological processes associated with brain development, craniofacial morphology, and cognitive behavior. Moreover, SVAs are among the most epigenetically de-repressed and transcriptionally upregulated TEs across a multitude of cancers. Our recent work demonstrated that the large majority of human-specific enhancers and promoters contain SVA insertions, and that SVA transposition within enhancer bodies correlates with either increased or decreased associated gene expression, with well-defined tissue-specific patterns. In spite of the conspicuous lines of evidence suggesting that SVAs are important regulators of human gene expression, we still have limited knowledge of the biology of these TEs. For example, we do not know the mechanism by which SVAs enhance AND repress transcriptional activity on host genes, tissues-specifically. We do not know which component(s) of the modular structure of these TEs drives the regulatory activity. Finally, and more importantly, we do not know the relative contribution of human-specific SVAs to the rewiring of human-specific regulatory networks, and to the generation of human specific traits. To fill these gaps of knowledge, we will apply our genomic expertise to human and chimpanzee's induced Pluripotent Stem Cell differentiation, using hippocampal neurogenesis as a proof of principle. Moreover, to address the mechanism, we will harness human cell-lines, CRISPR/Cas9, and genomics. We will deconstruct the complex modular architecture of SVAs, and define the mechanism adopted by SVAs to drive regulatory activity on the host genome. We will delve into the tissue-specific repressive activity displayed by select SVAs to uncover the underlying mechanism, also testing the hypothesis that a subset of SVAs offers a genome-wide substrate for a critical transcriptional repressor (YY1). With the proposed research we will gain transformative insights on how human-specific traits are generated, and we will shed light on why the dysregulation of SVAs is so frequently observed in disease, including cancer and neurological disorders.