PROJECT 1: SPATIOTEMPORAL GENOME ARCHITECTURE

项目1--基因组的时空结构 摘要 分子生物学的一个中心挑战是了解转录调控元件是如何 从基因组中选择，从而指定细胞身份和细胞特异性反应。在这个项目中，我们 将使用系统生物学方法和映射到模型的范例来深入了解 负责选择和发挥顺式调控要素的机制 对病原体的转录反应。这些活动包括以下四个具体目标。首先，我们 将生成一张地图，并使用它来模拟细胞特定增强子景观的选择。这个目标是 基于家族决定转录因子相对简单的组合的假设 (LDTF)在选择很大一部分细胞特异性增强剂方面起主导作用。我们将开发和测试 从全基因组预测巨噬细胞结合部位开始的机械性网络模型 LDTF和预测其他协同转录的全基因组结合位置的进展 影响增强剂选择的因素。其次，我们将对信号依赖的角色进行映射和建模 转录因子(SDTF)在调节增强子景观中的作用。这一目的是基于这样的假设 功能增强子的一个基本特征是它被主动转录。在这一目标中，我们将扩大 在目标1中开发的机制网络模型用于预测SDTF及其后续的结合 脂多糖暴露或腺病毒感染后增强子的转录激活。这个 模型的预测价值将通过对SDTF的功能损失研究和通过评估 自然遗传变异的影响。第三，我们将尝试预测转录活性作为以下因素的函数 增强相互作用。我们建议将目标2中实现的机械性网络模型扩展到考虑 空间共定位背景下的共同调控转录起始点。模型的这一方面将 通过评估功能缺失突变体和自然遗传变异对增强子的影响进行测试- 使用Hi-C分析的改进版本的启动子相互作用，该方法将测序能力集中在 涉及发起人的互动。最后，我们将绘制3D病毒-宿主基因组相互作用中心的地图并进行建模 以及决定跨组织和物种感染结果的转录网络。我们 假设病毒基因组靶向并颠覆宿主基因组的3D组织和相互作用 在感染过程中激活不同的病毒和宿主转录程序。建议数 研究将绘制和模拟3D基因组相互作用和不同组织内的转录程序 决定病毒嗜性和复制的类型。这些研究之所以特别有趣，是因为虽然 人腺病毒感染的早期程序在小鼠细胞中是完整的，它们的生产性裂解 复制/表达是通过鲜为人知的机制被“晚期”阻止的。一种分子 对这些机制的理解在概念和实践两个层面都具有重要意义。

PROJECT 1 – SPATIOTEMPORAL ARCHITECTURE OF THE GENOME SUMMARY A central challenge of molecular biology is to understand how transcriptional regulatory elements are selected from the genome thereby specifying cellular identity and cell-specific responses. In this project, we will use systems biology approaches and the maps-to-model paradigm to gain insights into general mechanisms responsible for the selection and function of cis-regulatory elements necessary for transcriptional responses to pathogens. These activities consist of the following four Specific Aims. First, we will generate a map and use this to model the selection of cell-specific enhancer landscapes. This aim is based on the hypothesis that relatively simple combinations of lineage-determining transcription factors (LDTFs) play dominant roles in selecting a large fraction of cell-specific enhancers. We will develop and test a mechanistic network model that begins with genome-wide predictions of binding sites for macrophage LDTFs and progresses to predict the genome-wide binding locations of other collaborating transcription factors that contribute to enhancer selection. Second, we will map and model the role of signal-dependent transcription factors (SDTFs) in regulating the enhancer landscape. This aim is based on the hypothesis that an essential feature of a functional enhancer is that it is actively transcribed. In this aim, we will extend the mechanistic network model developed in Aim 1 to predict binding of SDTFs and subsequent transcriptional activation of enhancers following lipopolysaccharide exposure or adenoviral infection. The predictive value of the model will be tested by loss-of-function studies of the SDTFs and by evaluation of effects of natural genetic variation. Third, we will try to predict transcriptional activity as a function of enhancer interactions. We propose extending the mechanistic network model achieved in Aim 2 to consider co-regulated transcriptional start sites in the context of spatial co-localization. This aspect of the model will be tested by evaluating loss-of-function mutants and the impact of natural genetic variation on enhancer- promoter interactions using a modified version of the Hi-C assay that focuses sequencing power on interactions involving promoters. Finally, we will map and model the 3D virus-host genome interaction hubs and transcriptional networks that determine the outcome of infection across tissues and species. We hypothesize that viral genomes target and subvert the 3D organization and interactions of the host genome to activate different viral and host transcriptional programs in the time course of infection. The proposed studies will map and model 3D genome interactions and transcriptional programs within different tissue types that determine viral tropism and replication. These studies are of particular interest because, while the `early' program of human adenovirus infection is intact in mouse cells, their productive lytic replication/expression is blocked `late' through mechanisms that are poorly understood. A molecular understanding of these mechanisms would be highly significant at both conceptual and practical levels.