Genome Architecture and Gene Control in Response to Stress

应对压力的基因组结构和基因控制

• 批准号: 10408736
• 负责人: David Samuel Gross
• 金额: $ 29.2万
• 依托单位: LOUISIANA STATE UNIV HSC SHREVEPORT
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10408736
• 关键词: 3-Dimensional; Acute; Address; Adopted; Architecture; Attenuated; Automobile Driving; Binding Sites; Biochemical; Biological; Biological Assay; Biological Models; Biological Process; Biology; Biophysics; Cells; Chromatin; Chromatin Interaction Analysis by Paired-End Tag Sequencing; Chromosomes; Clinical; Code; Complement; DNA-Directed RNA Polymerase; Development; Disease; Elements; Exposure to; Future; Gene Expression; Gene Proteins; Genes; Genetic; Genetic Techniques; Genetic Transcription; Genome; Genomics; Health; Heat shock factor; Heat shock proteins; Heat-Shock Response; Hi-C; Human; In Vitro; Laboratories; Liquid substance; Malignant - descriptor; Malignant Neoplasms; Mediating; Mediator of activation protein; Mission; Molecular; Molecular Conformation; Nature; Neurodegenerative Disorders; Nuclear; Organism; Phase; Phosphorylation; Play; Population; Process; Promoter Regions; Proteins; Regulation; Regulon; Role; Saccharomyces cerevisiae; Saccharomycetales; Specificity; Stress; System; Techniques; Terminator Regions; Testing; Therapeutic; Transcription Coactivator; Transcriptional Regulation; United States National Institutes of Health; Work; Yeasts; base; cell type; chromatin remodeling; chromosome conformation capture; cofactor; deep sequencing; experimental study; genome editing; genome-wide; heat-shock factor 1; in vivo; insight; member; novel; promoter; protein degradation; proteostasis; reconstitution; recruit; response; thermal stress; transcription factor; yeast genetics; yeast genome

1 Project Summary 2 3 The 3D topology of the genome plays a critical role in transcriptional regulation in health, disease and 4 development. While techniques such as Hi-C and ChIA-PET have revealed static views of global genome 5 architecture, very little is known about the mechanisms that control dynamic topological rearrangements. We 6 have established a system in budding yeast – the Hsf1-mediated heat shock response – in which concerted 7 structural rearrangements within and between a set of specific target genes take place. During heat shock, 8 Hsf1 drives its target genes dispersed on different chromosomes to undergo striking changes in conformation 9 and coalesce into discrete, transcriptionally active foci. These Hsf1 target genes encode a dedicated group of 10 protein homeostasis (proteostasis) factors. Through their regulation, the human orthologue of Hsf1 (hHSF1) 11 has been suggested to be a clinical target in malignant cancers and in neurodegenerative diseases. Thus, this 12 proposal has dual significance: it will both elucidate mechanisms that control chromatin conformational 13 dynamics and reveal how Hsf1 coordinates expression of the proteostasis machinery. 14 The Hsf1-mediated heat shock response in budding yeast represents an ideal model system to investigate 15 the regulation and function of 3D genome rearrangements for two reasons: 1) The magnitude, rapidity and 16 specificity of the intra- and intergenic rearrangements are all unprecedented and thus represent exciting, novel 17 biology; and 2) It will allow us to leverage the power of yeast gene-tics to dissect the mechanisms and define 18 the functional relevance of genome topology dynamics. 19 Aim 1 will investigate the 3D rearrangements that occur genome-wide during heat shock and the role 20 played by Hsf1 and RNA polymerase II (including its CTD phosphorylation state) in orchestrating specific and 21 robust interchromosomal contacts. The experiments will use primarily ChIA-PET approaches. 22 Aim 2 will focus deeply on the role of Hsf1 binding sites and its functional domains in underpinning its 23 ability to dynamically drive members of its regulon into coalesced intranuclear foci. 24 Aim 3 will test the role of Mediator and other cofactors - transcriptional co-activators, chromatin remodelers 25 and architectural proteins - in driving HSP gene coalescence and investigate the possibility that HSP gene 26 coalescence represents a condensate that assembles through liquid-liquid phase separation. 27 In support of the NIH mission, the precedents established in this proposal will inform therapeutic efforts 28 aimed broadly at 3D genome regulation and may suggest novel molecular handles with which to modulate 29 Hsf1 and the proteostasis machinery to treat cancer and neurodegenerative diseases.

1 项目概要 2 3 基因组的 3D 拓扑在健康、疾病和疾病的转录调控中发挥着关键作用 4 发展。虽然 Hi-C 和 ChIA-PET 等技术已经揭示了全球基因组的静态视图 5 架构中，人们对控制动态拓扑重排的机制知之甚少。我们 6 人在芽殖酵母中建立了一个系统——Hsf1 介导的热休克反应——其中协调一致 一组特定目标基因内部和之间发生 7 种结构重排。热休克期间， 8 Hsf1驱动分散在不同染色体上的靶基因发生显着的构象变化 9 并合并成离散的、转录活跃的焦点。这些 Hsf1 靶基因编码一组专用的 10 种蛋白质稳态（proteostasis）因素。通过它们的调节，Hsf1 的人类直系同源物 (hHSF1) 11已被认为是恶性癌症和神经退行性疾病的临床靶点。因此，这个 12提案具有双重意义：它将阐明控制染色质构象的机制 13 动力学并揭示 Hsf1 如何协调蛋白质稳态机制的表达。 14 芽殖酵母中 Hsf1 介导的热休克反应是研究的理想模型系统 15 3D 基因组重排的调控和功能有两个原因：1) 规模、速度和功能 16 基因内和基因间重排的特异性都是前所未有的，因此代表了令人兴奋的、新颖的 17 生物学； 2）它将使我们能够利用酵母遗传学的力量来剖析机制并定义 18 基因组拓扑动力学的功能相关性。 19 目标 1 将研究热休克过程中全基因组发生的 3D 重排及其作用 20 由 Hsf1 和 RNA 聚合酶 II（包括其 CTD 磷酸化状态）在协调特定和 21 个稳健的染色体间接触。实验将主要使用 ChIA-PET 方法。 22 目标 2 将深入关注 Hsf1 结合位点及其功能域在支撑其 23 能够动态驱动其调节子成员进入合并的核内病灶。 24 目标 3 将测试介体和其他辅助因子的作用 - 转录共激活因子、染色质重塑因子 25和结构蛋白-驱动HSP基因聚结并研究HSP基因的可能性 26聚结表示通过液-液相分离聚集的冷凝物。 27 为了支持 NIH 的使命，本提案中建立的先例将为治疗工作提供信息 28 广泛针对 3D 基因组调控，并可能提出用于调节的新分子手柄 29 Hsf1 和治疗癌症和神经退行性疾病的蛋白质稳态机制。