Mechanisms and functions of repressive chromatin structure in quiescent cells.

静止细胞中抑制性染色质结构的机制和功能。

• 批准号: 10542996
• 负责人: Sarah Grace Swygert
• 金额: $ 24.9万
• 依托单位: COLORADO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10542996
• 关键词: 3-Dimensional; Address; Appearance; Base Pairing; Basic Science; Binding; Biochemical; Bioinformatics; Biological Assay; Biological Models; CRISPR/Cas technology; Cells; ChIP-seq; Chromatin; Chromatin Loop; Chromatin Modeling; Chromatin Structure; Complex; DNA; Data; Electron Microscopy; Enhancers; Enzymes; Fiber; Foundations; Fred Hutchinson Cancer Research Center; Gene Cluster; Genes; Genetic Diseases; Genetic Transcription; Genomics; Histone Deacetylation; Histones; Human; Institutes; Knowledge; Link; Magnetism; Malignant Neoplasms; Maps; Mentors; Methods; Microscopy; Modeling; Molecular Conformation; Nucleosomes; Physical condensation; Physiological; Positioning Attribute; Process; Repression; Research; Research Personnel; Research Training; Resolution; Role; Saccharomyces cerevisiae; Structure; Supervision; System; Testing; Training; Transcriptional Regulation; Ursidae Family; Work; Yeasts; anticancer research; cancer cell; cancer drug resistance; cancer therapy; career; cohesin; condensin; developmental disease; electron tomography; experimental study; gene repression; genome-wide; human disease; interest; nanometer; promoter; single molecule; skills; three dimensional structure; transcription factor

Project Summary The conformation of chromatin is a primary mechanism by which the cell regulates DNA-templated processes. Consistent with this broad role, aberrations in the enzymes and structural components responsible for controlling chromatin dynamics have been linked to an extensive range of human diseases, including the majority of cancers and an increasing number of genetic and developmental disorders. Recent technological advancements have increased our knowledge of how the positions of nucleosomes on DNA are regulated and how chromatin forms large three-dimensional (3D) loops called chromatin domains. 3D chromatin structure is hypothesized to be capable of both promoting and inhibiting transcription depending on context. However, understanding the mechanisms and functions of these types of chromatin structures has been difficult due to the low resolution of current methods, which have made it almost impossible to determine chromatin structure within cells at scales necessary to determine its relationship to the expression of single-genes. As a result, the long-held hypothesis that 3D chromatin structure at this level regulates transcription has been largely untested in a physiological context. To examine 3D chromatin structure in cells in which it is expected to function extensively, the candidate has implemented a genomics method capable of mapping 3D chromatin structure genome-wide at unprecedented single-nucleosome 150 base pair resolution in quiescent S. cerevisiae. Quiescent yeast bear conserved hallmarks of quiescent cells, in particular widespread transcriptional repression and chromatin condensation, which make them an excellent model for determining the mechanisms by which 3D chromatin structure represses transcription. Preliminary results have led to the hypothesis that in quiescent cells, the condensin complex represses transcription by inducing quiescence-specific 3D chromatin structures. Aim 1 of this proposal will determine how condensin is targeted to form chromatin domains during quiescence using genomics, microscopy, and a single-molecule magnetic tweezer assay. Aim 2 will examine the conformation of chromatin within domains to determine if it is folded into 3D structure at a smaller scale and investigate whether chromatin structure at this scale is the mechanism by which transcription is repressed during quiescence. The mentored component of this work will be completed under the sponsorship of Dr. Toshio Tsukiyama, an expert in the chromatin field, at one of the premier institutes for basic science and cancer research, the Fred Hutchinson Cancer Research Center. The candidate will also be trained in single- molecule biochemical assays under the supervision of Dr. Sue Biggins, and will expand her proficiency in bioinformatics through coursework and independent study. This research and training will provide the candidate with an exciting model system and the skills necessary for a successful independent career.

项目概要 染色质的构象是细胞调节 DNA 模板的主要机制 流程。与这种广泛的作用相一致，负责的酶和结构成分的畸变 控制染色质动态的基因与多种人类疾病有关，包括 大多数癌症以及越来越多的遗传和发育障碍。最新技术 进步增加了我们对核小体在 DNA 上的位置如何调节和 染色质如何形成称为染色质域的大型三维 (3D) 环。 3D 染色质结构是 假设能够根据上下文促进和抑制转录。然而， 由于以下原因，理解这些类型的染色质结构的机制和功能一直很困难 当前方法的分辨率较低，几乎不可能确定染色质结构 在细胞内以必要的规模确定其与单基因表达的关系。结果， 长期以来一直持有的假设，即该水平的 3D 染色质结构调节转录，但在很大程度上尚未得到检验 在生理背景下。检查预期发挥功能的细胞中的 3D 染色质结构 候选人广泛地实施了一种能够绘制 3D 染色质结构的基因组学方法 在静止的酿酒酵母中以前所未有的单核小体 150 碱基对分辨率进行全基因组分析。 静止酵母具有静止细胞的保守特征，特别是广泛的转录特征 抑制和染色质浓缩，这使它们成为确定机制的绝佳模型 3D 染色质结构通过其抑制转录。初步结果得出这样的假设： 在静止细胞中，凝缩蛋白复合物通过诱导静止特异性 3D 染色质来抑制转录 结构。该提案的目标 1 将确定凝缩蛋白如何靶向形成染色质结构域 使用基因组学、显微镜和单分子磁镊测定进行静止。目标 2 将检查 域内染色质的构象，以确定其是否以较小的尺度折叠成 3D 结构 并研究这种规模的染色质结构是否是转录被抑制的机制 静止期间。这项工作的指导部分将在博士的赞助下完成。 月山俊夫 (Toshio Tsukiyama) 是染色质领域的专家，就职于一流的基础科学研究所之一 癌症研究，弗雷德·哈钦森癌症研究中心。候选人还将接受单项培训 在 Sue Biggins 博士的监督下进行分子生化分析，并将扩大她在以下方面的熟练程度 通过课程作业和独立学习进行生物信息学。这项研究和培训将提供 候选人拥有令人兴奋的模型系统和成功的独立职业所需的技能。