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: 10002245
• 负责人: Sarah Grace Swygert
• 金额: $ 10万
• 依托单位: FRED HUTCHINSON CANCER RESEARCH CENTER
• 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 2021-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10002245
• 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; 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; enzyme structure; 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.

项目摘要 染色质的构象是一种主要机制 过程。与这种广泛的作用，酶的畸变和负责的结构成分一致 用于控制染色质动力学已与广泛的人类疾病有关，包括 大多数癌症以及越来越多的遗传和发育障碍。最近的技术 进步已经提高了我们对核小体在DNA中的位置的了解，并 染色质如何形成称为染色质结构域的大型三维（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， 由于了解这些类型的染色质结构的机制和功能很困难 当前方法的低分辨率，这几乎无法确定染色质结构 在细胞内的尺度中，确定其与单生成表达的关系所必需的。结果， 长期以来的假设是，在此级别调节转录的3D染色质结构已在很大程度上未经测试 在生理环境中。在细胞中检查3D染色质结构，预计会发挥作用 广泛地，候选人实施了能够绘制3D染色质结构的基因组学方法 在静态的S. cerevisiae中，在前所未有的单核体150碱基对分辨率下，全基因组在全基因组中。 静态酵母菌熊保守的静态细胞的标志，特别是广泛的转录 抑制和染色质凝结，这使它们成为确定机制的绝佳模型 3D染色质结构抑制转录。初步结果导致了以下假设 静态细胞，冷凝蛋白复合物通过诱导静止特异性3D染色质抑制转录 结构。该提案的目的1将决定如何将凝蛋白靶向以形成染色质结构域 使用基因组学，显微镜和单分子磁性镊子测定法。 AIM 2将检查 染色质在域内的构象，以确定它是否以较小的比例折叠成3D结构 并研究该量表的染色质结构是否是抑制转录的机制 在静止期间。这项工作的指导部分将在博士的赞助下完成。 Toshio Tsukiyama是染色质领域的专家，位于基础科学的一所主要机构和 癌症研究，弗雷德·哈钦森癌症研究中心。候选人还将接受单一培训 在Sue Biggins博士的监督下，分子生化测定 通过课程和独立研究的生物信息学。这项研究和培训将为 具有令人兴奋的模型系统的候选人以及成功独立职业所需的技能。