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

揭示转录和染色质 3D 结构在细胞激活过程中如何相互影响

基本信息

批准号：
10389952
负责人：
Christopher W Benner
金额：
$ 3.6万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-16 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10389952
关键词：
3-Dimensional Acute Address Affect Area Binding Sites Biomedical Research Cell Nucleus Cells Chromatin Chromatin Loop Communication Consensus DNA DNA Packaging Data Dissociation Distal Enhancers Etiology Gene Activation Gene Expression Gene Expression Profile Genes Genetic Enhancer Element Genetic Models Genetic Transcription Genome Heat-Shock Response Infection Influenza A virus Interferon-beta Ligands Measurement Measures Mediating Minor Play Poly I-C Process Processed Genes RNA Polymerase II Reagent Regulation Regulatory Element Reporting Role Stimulus Structure TLR3 gene Techniques Testing Transcription Elongation Transcription Initiation Transcriptional Activation Transcriptional Regulation Virus Diseases base cell type cohesin gene induction gene repression genome-wide improved inducible gene expression inhibitor/antagonist programs promoter recruit response temporal measurement three dimensional structure

项目摘要

Summary (original application): The 3D organization 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 may have a relatively minor impact on gene expression, challenging the generality of this paradigm. In fact, most studies 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 have 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. Our 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 strong transcriptional stimuli. By profiling nascent transcription initiation (csRNA-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. These studies will reveal how chromatin 3D structure and transcription influence each other and will help improve the interpretation of regulatory programs encoded in the genome.

摘要（原始申请）：细胞核内染色质的 3D 组织被认为在基因调节中发挥着重要作用表达。通常认为启动子、增强子和其他关键调控元件发挥作用通过在 DNA 中形成环，使关键调控元件在空间上紧密相连来产生影响。然而，最近的研究表明 DNA 环可能对基因表达的影响相对较小，挑战这种范式的普遍性。事实上，大多数调查基因之间关系的研究表达和基因组 3D 结构依赖于相关测量，通常缺乏直接证据表明空间 DNA 相互作用对基因表达产生影响。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连蛋白来直接影响基因组 3D 结构染色质，导致 DNA 环丢失。我们的研究结果和其他报告表明我们缺乏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对于解释至关重要调控程序如何在基因组中编码，并对基因组研究产生重要影响几乎在生物医学研究的所有领域发挥作用。该提案利用了最近开发的试剂和敏感的分析技术来研究基因组 3D 结构如何影响转录，并且反过来，转录如何影响基因组 3D 结构以响应强转录刺激。通过分析新生转录起始 (csRNA-seq)，我们将系统地描述染色质环丢失是如何发生的影响启动子和增强子元件的诱导转录，并检查 3D 的扰动如何结构影响远端调控元件与其靶基因之间的功能通讯。这该提案还将探讨转录激活本身如何调节染色质环的形成或解离。这些研究将揭示染色质 3D 结构和转录如何相互影响以及将有助于改善对基因组中编码的调控程序的解释。