High resolution chromatin structure of purified eukaryotic genes

纯化真核基因的高分辨率染色质结构

• 批准号: 10014622
• 负责人: Robert Kenneth Louder
• 金额: $ 6.53万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-16 至 2022-09-15
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10014622
• 关键词: 3-Dimensional; Address; Adopted; Architecture; Biochemistry; Biological; Biological Assay; Cell Cycle; Cell Nucleus; ChIP-seq; Chemicals; Chromatin; Chromatin Structure; Code; Complex; Cryo-electron tomography; Cryoelectron Microscopy; DNA; Detection; Dimensions; Disease; Electron Microscopy; Environment; Eukaryota; Functional disorder; Galectin 1; Gene Expression; Gene Transfer; Generations; Genes; Genetic Transcription; Genome; Genomic DNA; Goals; Histones; In Situ; In Vitro; Individual; Isotope Labeling; Malignant Neoplasms; Maps; Mass Spectrum Analysis; Measurement; Methods; Modeling; Modernization; Modification; Molecular Conformation; Mutation; Nature; Negative Staining; Nucleic Acid Regulatory Sequences; Nucleosomes; Phase; Plasmids; Play; Population; Population Statistics; Positioning Attribute; Preparation; Promoter Regions; Proteins; Proteomics; Quality Control; Regulatory Pathway; Research; Resolution; Role; Saccharomyces cerevisiae; Sampling; Structure; System; Techniques; Testing; Three-dimensional analysis; Time; Transcriptional Regulation; Universities; Work; Yeasts; chromatin modification; chromosome conformation capture; crosslink; genetic manipulation; genome-wide; genomic locus; high resolution imaging; human disease; in vivo; insight; instrumentation; nervous system disorder; non-histone protein; nuclease; particle; preservation; protein folding; reconstitution; reconstruction; single molecule; structural biology; three dimensional structure; three-dimensional visualization; two-dimensional

PROJECT SUMMARY/ABSTRACT In eukaryotes, genomic DNA is condensed into chromatin by associating with histone proteins, and the folding of chromatin organizes the genome within the cell nucleus and plays an essential role in regulating gene transcription. Chromatin dysfunction and the resulting dysregulation of gene expression is a well-recognized contributor to many human diseases, including cancers and neurological disorders. Despite decades of research and its crucial role in the expression of genes, the native chromatin structure of coding and regulatory regions of the genome remains poorly resolved. While conventional structural biology methods have yielded many high- resolution structures of chromatin components, a general limitation of these studies is that the conditions used to prepare samples in vitro do not faithfully recapitulate the native chromatin environment in vivo, due to complex and variable composition of native chromatin. On the other hand, methods that have been geared towards probing the native chromatin landscape in situ are well-suited to provide information of a broad scale (e.g. genome wide) but are limited in resolution or dimensionality. I aim to bridge the gap between these traditional approaches by analyzing the composition and structure of natively assembled, yet purified, chromatin of specific yeast gene loci. The initial phase of this work will be aimed at optimizing the preparation of isolated chromosomal fragments in order to maximize preservation of their native composition and structure, using a combination of electron microscopy (EM) and mass spectrometry proteomics as quality control assays. Quantitative mass spectrometry of isotope-labeled samples will also be used to perform “chromatin proteomics” by analyzing changes in chromatin composition between the induced and repressed forms of the minichromosome genes. Following optimization of purification conditions, negative stain and rotary shadowing EM will be used to generate high-resolution two-dimensional maps of nucleosome positioning across populations of a given purified yeast gene in its active or repressed state. Finally, utilizing state-of-the-art instrumentation available at Johns Hopkins University, modern cryo-EM and cryo-electron tomography techniques will be used to analyze the three- dimensional chromatin structure of the purified gene, including an assessment of the variability in chromatin structure amongst populations of repressed or induced genes. Ultimately, this approach should provide an overview of the three-dimensional “structure” of a gene in both repressed and activated states, as well as “zoomed-in” views of specific gene fragments, showing for instance the interplay between histones and non- histone proteins at the promoter region of genes. The results of this study will significantly advance our understanding of the mechanisms behind transcriptional regulation via chromatin, and could provide insights into mechanisms of transcriptional dysregulation that cause disease.

项目总结/摘要 在真核生物中，基因组DNA通过与组蛋白蛋白结合而浓缩成染色质， 染色质的折叠在细胞核内组织基因组，并在调节基因表达中起重要作用。 转录。染色质功能障碍和由此导致的基因表达失调是一个公认的 它是许多人类疾病的罪魁祸首，包括癌症和神经系统疾病。尽管经过几十年的研究 及其在基因表达中的关键作用，编码和调节区域的天然染色质结构， 基因组的解析度仍然很低。虽然传统的结构生物学方法已经产生了许多高- 染色质组分的分辨率结构，这些研究的一般限制是所使用的条件 在体外制备样品并不能忠实地再现体内天然染色质环境， 和天然染色质的可变组成。另一方面，已经调整的方法 原位探测天然染色质景观非常适合于提供大规模的信息（例如， 全基因组），但分辨率或维度有限。我的目标是弥合这些传统之间的差距 方法通过分析天然组装，但纯化，染色质的组成和结构， 酵母基因座这项工作的初始阶段将旨在优化分离的染色体的制备。 为了最大限度地保留其天然成分和结构，使用以下组合 电子显微镜（EM）和质谱蛋白质组学作为质量控制测定。定量质量 同位素标记样品的光谱分析也将用于通过分析 微小染色体基因的诱导和抑制形式之间的染色质组成的变化。 在优化纯化条件后，将使用负染和旋转阴影EM来产生 给定纯化酵母菌群间核小体定位的高分辨率二维图谱 处于活跃或压抑状态的基因。最后，利用约翰霍普金斯大学最先进的仪器 大学，现代冷冻EM和冷冻电子断层扫描技术将被用来分析这三个- 纯化基因的三维染色质结构，包括染色质变异性的评估 抑制或诱导基因群体之间的结构。最终，这种方法应该提供一个 概述了基因在受抑制和激活状态下的三维“结构”，以及 特定基因片段的“放大”视图，显示例如组蛋白和非组蛋白之间的相互作用。 基因启动子区域的组蛋白。这项研究的结果将大大促进我们的 通过染色质转录调控背后的机制的理解，并可以提供见解， 导致疾病的转录失调机制。