Uncovering how transcription and chromatin 3D structure impact one another during cellular activation

项目摘要/摘要： 核内染色质的3D包装被认为在基因调控中起着重要作用 表情。人们通常认为，启动者、增强剂和其他关键的监管要素 通过在DNA中形成环，使关键调控元件在空间上接近而产生影响。然而， 最近的研究表明，DNA环对基因表达的影响相对较小，挑战了 这个范例的概括性。事实上，大多数研究基因和基因之间关系的实验 表达和基因组3D结构依赖于相关的测量，通常缺乏直接证据 空间DNA相互作用对基因表达有影响。相比之下，我们最近发现 转录延伸可以通过取代环状分子粘附素直接影响基因组3D结构 从染色质中分离出来，导致DNA环丢失。这些发现和其他报告表明，我们缺乏一个 充分了解染色质循环如何参与基因表达程序的执行。一个 更详细地了解基因组3D结构和转录如何相互调节是解释基因组3D结构和转录的关键 调控程序是如何在基因组中编码的，并对研究基因组有重要影响 在生物医学研究的几乎所有领域发挥作用。这项建议利用了最近开发的试剂和 灵敏的图谱技术，研究基因组3D结构如何影响转录，反过来， 转录如何影响基因组3D结构对急性细胞刺激的反应。使用初生的 启动图谱(START-SEQ)，我们将系统地表征染色质环的丢失如何影响 在启动子和增强子元件上均可诱导转录，并研究3D结构的扰动 影响远端调控元件与其靶基因之间的功能通讯。这项建议 我还将探索转录激活本身如何调节染色质环的形成或解离 转录变化的直接后果。这些研究将有助于揭示染色质3D结构和 转录相互影响，将有助于改进对编码的调控程序的解释 基因组。

Project Summary/Abstract: The 3D packaging of chromatin within the nucleus is thought to play an important role in regulating gene expression. It is often assumed that promoters, enhancers, and other critical regulatory elements exert influence by forming loops in DNA that bring key regulatory elements into close spatial proximity. However, recent studies have shown that DNA loops have a relatively minor impact on gene expression, challenging the generality of this paradigm. In fact, most experiments that investigate the relationship between gene expression and genome 3D structure rely on correlated measurements and usually lack direct evidence that spatial DNA interactions have an impact on gene expression. In contrast, we recently discovered that transcription elongation can directly impact genome 3D structure by displacing the ring-like molecule cohesin from chromatin, leading to the loss of DNA loops. These findings and other reports suggest that we lack an adequate understanding of how chromatin looping is involved in the execution of gene expression programs. A more detailed view of how genome 3D structure and transcription regulate one another is essential to interpret how regulatory programs are encoded in the genome, and has important consequences for studying genome function in nearly all areas of biomedical research. This proposal leverages recently developed reagents and sensitive profiling techniques to investigate how genome 3D structure impacts transcription and, reciprocally, how transcription impacts genome 3D structure in response to acute cellular stimulation. Using nascent initiation profiling (Start-seq), we will systematically characterize how loss of chromatin looping impacts inducible transcription at both promoter and enhancer elements and examine how perturbation of 3D structure impacts the functional communication between distal regulatory elements and their target genes. This proposal will also explore how transcriptional activation itself may regulate chromatin loop formation or dissociation as a direct consequence of changes in transcription. These studies will help reveal how chromatin 3D structure and transcription influence each other and will help improve the interpretation of regulatory programs encoded in the genome.