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: 10633221
• 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 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10633221
• 关键词: 3-Dimensional; Acute; Address; Adopted; Architecture; 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; Dedications; Development; Disease; Disparate; Elements; Exposure to; Future; Gene Expression; Gene Proteins; Genes; Genetic; Genetic Techniques; Genetic Transcription; Genome; Genomics; Health; Heat shock proteins; Heat-Shock Response; Hi-C; Human; In Vitro; Laboratories; Liquid substance; Malignant - descriptor; Malignant Neoplasms; Mediating; Mediator; Mission; Molecular; Molecular Conformation; Nature; Neurodegenerative Disorders; Nuclear; Organism; Phase; Phosphorylation; Physical condensation; 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; cell type; 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拓扑结构在健康、疾病和疾病的转录调控中起着关键作用。 4发展。虽然Hi-C和ChIA-PET等技术揭示了全球基因组的静态视图， 5架构，很少有人知道的机制，控制动态拓扑重排。我们 6已经在芽殖酵母中建立了一个系统--Hsf 1介导的热休克反应--其中协调 7一组特定靶基因内部和之间发生结构重排。在热休克期间， 8 Hsf 1驱动分散在不同染色体上的靶基因发生显著的构象变化 9和合并成离散的，转录活性灶。这些Hsf 1靶基因编码一组专用的 10种蛋白质稳态（proteostasis）因子。通过它们的调节，人类Hsf 1（hHSF 1）的直向同源物 11已被认为是恶性癌症和神经退行性疾病的临床靶标。因此，这 12的建议具有双重意义：它将阐明控制染色质构象的机制， 13动力学，并揭示Hsf 1如何协调蛋白质稳定机制的表达。 14芽殖酵母中Hsf 1介导的热休克反应是研究的理想模型系统 3D基因组重排的调节和功能有两个原因：1）3D基因组重排的幅度、速度和 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 图18基因组拓扑动力学的功能相关性。 19 Aim 1将研究在热休克过程中发生的全基因组3D重排及其作用。 20由Hsf 1和RNA聚合酶II（包括其CTD磷酸化状态）在协调特异性和 21个染色体间接触。这些实验将主要使用ChIA-PET方法。 22目标2将深入关注Hsf 1结合位点及其功能结构域在支持其功能中的作用。 23动态驱动其调节子成员进入合并的核内病灶的能力。 24目标3将测试中介子和其他辅因子的作用-转录辅激活因子，染色质重塑因子 25和结构蛋白-在驱动HSP基因聚结中的作用，并研究HSP基因 26聚结表示通过液-液相分离聚集的冷凝物。 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，并可能提出新的分子手柄， 29 Hsf 1和蛋白质稳定机制治疗癌症和神经退行性疾病。