DNA Information and Organization at Supranucleosomal Scales

项目3试图揭示高阶染色质结构和与癌症相关的基因调控机制之间的联系。细胞分化与广泛的基因组沉默有关，通常伴随着“兼性异染色质”的形成，即染色质更紧密(更折叠)的状态。基因组DNA序列中可能显式地编码了本质上较好的高阶结构。高阶结构的一个重要效果可能是可以定义复制的起源，并且 由染色质结构调节，而不是由特定的DNA序列元件调节。染色质高阶结构的变化可能出现在癌前组织中，这表明一种假说，即光学检测用于癌症诊断的“场效应”可能源于对异染色质的数量和分布的测量。回答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。这将允许理解与启动恶性肿瘤相关的基本染色体组织变化，然后导致在建立新的诊断工具时使用这些变化。要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，包括使用蛋白质特定的纳米颗粒标记技术来成像染色质结构域；对亚微米级活细胞染色质结构域中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微操作研究； 以及用于检测染色质蛋白质翻译后修饰的高分辨率质谱学。数据将用于构建定量模型，了解序列特征如何与高阶染色质结构相关并控制癌细胞中的高阶染色质结构，以及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 将阐明高水平信息层的存在和传递方式，部分是遗传的，部分是表观遗传的，参与癌症发展过程中染色质结构和基因表达的转换。

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.