Regulatory elements of replication timing and 3D genome organization

项目摘要 越来越多的证据表明，3D基因组结构是调节基因功能所必需的， 改变与许多疾病有关。基因组被组织成间隔排列 与DNA复制的时间顺序（复制时间- RT）。然而，人们对此知之甚少。 RT控制和3D基因组组织的潜在机制。最近，我们发现了一个新的类， 控制RT和3D基因组组织的顺式调控元件：早期复制控制 元素-ERCE。我们的长期目标是研究基因组的调控元件是什么 组织在人类分化的细胞类型，调查如何反式作用因子控制这些 元素，并定义了3D基因组组织在发育和进化过程中如何重塑。到 为了实现这些目标，我们正在删除和插入候选ERCE到人类基因组中， 分化的细胞类型，并测试它们对RT、3D基因组组织和基因表达的影响。 我们还利用高度同步的人类胚胎干细胞分化系统来跟踪 ERCE在细胞命运定型过程中的激活。最后，为了更好地理解基因组是如何 在进化过程中重塑，我们正在进行3D基因组组织的比较分析， 使用来自不同物种的原代细胞发挥功能。在这个项目中，我们将利用最先进的 基因组技术与自动化和可扩展的下一代测序文库相结合 制备平台，以研究RT，基因组结构和基因 表情总的来说，我们希望我们的工作将大大有助于理解基本的 基因组组织的原则及其与基因功能的关系。

PROJECT SUMMARY Increasing evidence indicates that 3D genome architecture is required to regulate gene function and its alterations are associated with many diseases. The genome is organized into compartments that align with the temporal order of DNA replication (replication timing – RT). However, little is known about the mechanisms underlying RT control and 3D genome organization. Recently, we identified a novel class of cis regulatory elements that control RT and 3D genome organization: early replicating control elements – ERCEs. Our long-term goals are to study what are the regulatory elements of genome organization in human differentiated cell types, investigate how trans-acting factors control these elements, and define how 3D genome organization is remodeled during development and evolution. To achieve these goals, we are deleting and inserting candidate ERCEs into the genome of human differentiated cell types and testing their effects on RT, 3D genome organization and gene expression. We are also exploiting highly synchronous human embryonic stem cells differentiation systems to track ERCE activation during cell fate commitment. Finally, to better understand how the genome was remodeled during evolution, we are performing comparative analyses of 3D genome organization and function using primary cells derived from different species. In this project, we will exploit state-of-the-art genomic technologies combined with automated and scalable next-generation sequencing library preparation platforms to investigate the connections between RT, genome architecture and gene expression. Overall, we expect that our work will contribute significantly to understand the fundamental principles of genome organization and its relationship to gene function.