Regulatory elements of replication timing and 3D genome organization

项目总结 越来越多的证据表明，3D基因组结构需要调节基因的功能和它的 改变与许多疾病有关。基因组被组织成对齐的隔间 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别 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-ERCEs。我们的长期目标是研究基因组的调控元件是什么 在人类分化的细胞类型中的组织，研究反式作用因子如何控制这些 元素，并定义3D基因组组织在发展和进化过程中是如何重塑的。至 为了实现这些目标，我们正在删除候选ERCEs并将其插入人类基因组 分化的细胞类型及其对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追踪 ERCE在细胞命运承诺过程中的激活。最后，为了更好地了解基因组是如何 在进化过程中进行了重塑，我们正在进行3D基因组组织和 使用来自不同物种的原代细胞来发挥功能。在这个项目中，我们将利用最先进的技术 基因组技术与自动化和可扩展的下一代测序库相结合 研究RT、基因组结构和基因之间关系的准备平台 表情。总体而言，我们预计我们的工作将大大有助于理解 基因组组织原理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.