Stability of the folded genome

项目总结 基因组结构缺陷引起的正常基因表达的干扰可能会导致 与衰老和各种疾病状态有关的细胞功能障碍。哺乳动物的基因组通常是 被组织成染色体、隔室、拓扑相关结构域(TADS)和环路。虽然 TAD和环的形成已被广泛研究，但对驱动核的过程知之甚少 车厢队形。已经有人提出，微相分离推动了 类似染色质状态的基因组结构域，导致形成A型(活性染色质)或B型 (非活性染色质)隔室。然而，由于缺乏工具，识别涉及的因素一直受到限制 能够量化驱动这一现象的生物物理性质。 哺乳动物异染色质蛋白1(Hp1)α和hp1β结合结构型异染色质， 有助于核小体之间的桥联，这表明这些蛋白质在 异染色质区划。尽管最近的一项研究表明，异染色质 紧凑作用独立于Hp1α，我们的合作者的工作表明，这种蛋白质是必需的 稳定异色基因座之间的相互作用。有趣的是，HP1蛋白和它们的几个相互作用 合作伙伴可以绑定RNA。与HP1功能无关，已知特定的RNA转录本发挥重要作用 在空间基因组组织的形成和维持以及可能的微相分离中的作用， 特别是在雌性细胞的核仁、斑点和不活跃的X染色体上。 我们最近开发了液体染色质Hi-C(LC-Hi-C)，它可以对染色质进行定量 在全基因组范围内测量相互作用稳定性。简而言之，孤立的核受到原位限制。 消化。将基因组消化成特定的片段大小分布会导致Low 密度/不稳定的相互作用，而保持较高的密度/稳定的相互作用，这是可以量化的 通过全基因组染色体构象捕获(Hi-C)。这项技术揭示了溶解动力学 染色质相互作用的大小在A和B隔室以及隔室亚结构之间变化很大。 目标1中“原位LC-HIC”的发展将使有丝分裂染色体的稳定性测量成为可能， 简化现有的方案，并允许研究较小的细胞群体。目标2将评估捐款 (Hp1)α和hp1β对异色相互作用稳定性的影响。在目标3中，LC-Hi-C将允许识别 基因组区域因RNA耗尽而不稳定。随后将确定有助于稳定的候选因素。 使用原位染色质相关RNA测序(IMARGI)，并通过扰动和LC-Hi- 总之，这项研究旨在测量染色质相互作用的动力学，并提供新的 对基因组在整个细胞周期中如何组织的机械论洞察力。

PROJECT SUMMARY Perturbations in normal gene expression arising from defects in genome organization can lead to cellular dysfunctions linked to aging and various disease states. The mammalian genome is generally organized into chromosomes, compartments, topological associating domains (TADs) and loops. Although TAD and loop formation have been extensively studied, little is known about the processes that drive nuclear compartment formation. It has been proposed that microphase phase separation drives the association of genomic domains of similar chromatin state, resulting in the formation of either type A (active chromatin) or B (inactive chromatin) compartments. However, identifying factors involved has been limited by a lack of tools capable of quantifying the biophysical properties driving this phenomenon. Mammalian heterochromatin protein 1 (HP1) α and HP1β bind constitutive heterochromatin and are known to facilitate the bridging of nucleosomes, suggesting that these proteins play a key role in heterochromatin compartmentalization. Although a recent study has demonstrated that heterochromatin compaction is independent of HP1α, work from our collaborators suggest that this protein is required to stabilize interactions between heterochromatic loci. Interestingly, HP1 proteins and several of their interacting partners can bind RNAs. Independent of HP1 function, specific RNA transcripts are known to play important roles in the formation and maintenance of spatial genome organization and perhaps microphase separation, notably at nucleoli, speckles, and the inactive X chromosome of female cells. We recently developed liquid chromatin Hi-C (LC-Hi-C), which allows quantification of chromatin interaction stability measurements genome-wide. Briefly, isolated nuclei are subject to in situ restriction digestion. Digestion of the genome into a specific fragment size distribution results in the loss of low density/unstable interactions whereas higher density/stable interactions are maintained, which is quantifiable by genome-wide chromosome conformation capture (Hi-C). This technique reveals that the dissolution kinetics of chromatin interactions vary widely between A and B compartments as well as compartmental substructures. The development of “in situ LC-HiC” in Aim 1 will allow stability measurement on mitotic chromosomes, streamline the existing protocol and allow the study of smaller cell populations. Aim 2 will assess contributions of (HP1) α and HP1β to stability of heterochromatic interactions. In Aim 3, LC-Hi-C will allow identification of genomic regions destabilized by RNA depletion. Candidate factors contributing to stability will then be identified using in situ chromatin-associated RNA sequencing (iMARGI) and validated by perturbation followed by LC-Hi- C. Taken together, this study aims to measure the dynamics of chromatin interactions and to provide new mechanistic insight as to how the genome is organized throughout the cell cycle.