? Data Analysis and Modeling Despite the growing quantity and resolution of chromosome interaction data our understanding of physical principles underling chromosomal organization and its connection with genomic function remain limited. Mapping of chromosomal interactions proposed in Component 2, will provide large amounts of data from a variety of methods that each address its own aspect and range of scales of chromosomal organization. Further progress, however, relies on our ability to bridge between these new data and 3D physical models of chromosomes that can reveal principles of genome folding. We will continue development of methods for processing, correction and analysis of data from Hi-C- based technologies, as well as development of polymer models of chromosomal organization that have been successful in reproducing Hi-C and microscopy data for human and bacterial chromosomes, and have been able to reveal structural elements not immediately visible in the data. Here we propose to take a full advantage of the new mapping technologies and further develop our physics-based approach to address several challenges in understanding biological mechanisms and physical principles of chromosomes folding. Modeling will also provide a natural platform for integration of interaction and imaging data. First, we will develop computational tools for processing data produced by new Hi-C-based technologies, (micro-C, high-resolution Hi-C, allele-specific Hi-C and single-cell Hi-C), and integrate data across scales into Integrated Interaction Maps. Second, we will develop computational tools to analyze Interaction Maps produced by new Hi-C-based technologies, aiming to reveal structural elements of human chromosomes at different scales. Third, we will develop polymer models that will allow validation of Hi-C interaction maps by HIPMap microscopy data, as proposed in Component 2. Finally, we will develop a comprehensive multi-scale polymer model of human chromosomal organization, comparing it to new interaction data at every scale. All models and discovered principles of organization will be systematically validated using imaging, genome engineering, and micromechanical experiments as outlined in Components 4 and 5.
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