DNA Information and Organization at Supranucleosomal Scales

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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.