DNA Information and Organization at Supranucleosomal Scales

核小体上尺度的 DNA 信息和组织

• 批准号: 8182399
• 负责人: JOHN F MARKO
• 金额: $ 29.91万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8182399
• 关键词: Adhesions; Architecture; Binding; Biological Models; Cancer Model; Cancerous; Cell Cycle; Cell Differentiation process; Cell Nucleus; Cells; Chemicals; Chromatin; Chromatin Fiber; Chromatin Structure; Chromosome Structures; Chromosomes; Code; Complex; DNA; DNA Binding; DNA Sequence; DNA replication origin; Data; Dependence; Detection; Development; Diffuse; Disease; Electron Microscopy; Elements; Epigenetic Process; Euchromatin; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genome; Genomics; Heterochromatin; Higher Order Chromatin Structure; Histones; Image; Imaging Techniques; Interphase Chromosome; Label; Lasers; Lead; Length; Life; Lighting; Link; Malignant Neoplasms; Mass Spectrum Analysis; Measurement; Measures; Mechanics; Metals; Metaphase; Methods; Micromanipulation; Microscopy; Modeling; Nuclear; Nuclear Extract; Nucleosomes; Optics; Outcome; Pattern; Positioning Attribute; Post-Translational Protein Processing; Premalignant; Premalignant Cell; Property; Proteins; RNA Interference; Replication Origin; Repression; Resolution; Role; Sampling; Science; Spottings; Stretching; Techniques; Testing; Texture; Tissues; Topoisomerase II; Translations; Variant; base; cancer cell; cancer diagnosis; cell behavior; chromatin protein; cohesin; condensin; density; flexibility; gene repression; histone modification; information organization; insight; knock-down; light scattering; model development; nanoparticle; novel diagnostics; protein folding; reconstitution; research study; single molecule; submicron; technology development; three dimensional structure; tool; transcription factor

Project 3 seeks to uncover the connection between higher-order chromatin structure and gene regulation mechanisms relevant to cancer. Cellular differentiation is linked to silencing of broad groups of genes, often with accompanying formation of "facultative heterochromatin", a more-compact (more-folded) state of chromatin. Intrinsically preferred higher order structures may be explicitly encoded in genomic DNA sequence. An important effect of higher-order structure may be that origins of replication can be defined and regulated by chromatin structure, rather than by specific DNA sequence elements. Changes in higher order structure in chromatin may appear in precancerous tissue, suggesting a hypothesis that optical detection of the "field effect" used in cancer diagnosis may follow from measurement of amounts and distribution of heterochromatin. Answering these questions depends on development of technologies for physical analyses of nuclear and chromatin structure, and then on application of them to cancer model systems. This will allow understanding the basic chromosome organization changes associated with turning on malignancy, and then lead to use of those changes in establishment of new diagnostic tools. Physical tools to be used include chemically sensitive and high-resolution electron microscopy methods from materials science, including use of protein-specific nanoparticle labeling techniques to image chromatin domains; non-imaging light-scattering techniques sensitive to variations and textures in chromatin domains in live cells at submicron length scales; single-molecule, single-chromosome, and single-genome micromanipulation studies of chromatin folding; and high-resolution mass spectroscopy for detection of post translational modifications of chromatin proteins. Data will be used in construction of quantitative models of how sequence features are correlated with and control higher-order chromatin structure and how that control is modified in cancerous cells, and understanding of how spatially correlated patterns of global repression impact cell cycle dynamics. The result will be illumination ofthe existence and modes of transfer of a high-level layer of information, partially genetic and partially epigenetic, involved in switching of chromatin structure and gene expression during development of cancer.

项目3旨在揭示高阶染色质结构与癌症相关基因调控机制之间的联系。细胞分化与大量基因的沉默有关，通常伴随着“兼性异染色质”的形成，这是一种更紧凑（更多折叠）的染色质状态。基因组DNA序列中可以明确编码内部优先的高级结构。高阶结构的一个重要影响可能是可以定义复制起点， 由染色质结构调控，而不是由特定的DNA序列元件调控。癌前组织中可能出现染色质中高阶结构的变化，这表明了一种假设，即用于癌症诊断的“场效应”的光学检测可能来自异染色质的量和分布的测量。解决这些问题有赖于物理分析技术的发展 核和染色质结构，然后将它们应用于癌症模型系统。这将允许理解与恶性肿瘤相关的基本染色体组织变化，然后导致使用这些变化建立新的诊断工具。使用的物理工具包括 来自材料科学的化学敏感和高分辨率电子显微镜方法，包括使用蛋白质特异性纳米颗粒标记技术来成像染色质结构域;对亚微米长度尺度的活细胞中染色质结构域的变化和纹理敏感的非成像光散射技术;染色质折叠的单分子、单染色体和单基因组显微操作研究; 以及用于检测染色质蛋白的翻译后修饰的高分辨率质谱。数据将用于构建序列特征如何与高阶染色质结构相关并控制高阶染色质结构以及如何在癌细胞中修改控制的定量模型，并了解空间相关的全局抑制模式如何影响细胞周期动力学。结果 将是照明的存在和高层次的信息传递模式，部分遗传和部分表观遗传，参与染色质结构和基因表达在癌症发展过程中的开关。