Center for 3D Structure and Physics of the Genome

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PROJECT SUMMARY The dynamic three-dimensional folding of the human genome within the cell nucleus, referred to as the 4D nucleome, plays roles in many genomic processes, including gene regulation and maintenance of genome stability. Defects in chromosome organization are associated with human diseases such as cancer, and premature aging. The 4D nucleome is extensively re-organized as cells change state during development and as cells age. In order to understand how the genome works we need comprehensive maps of the 4D nucleome for different cell states. We also need detailed knowledge of the molecular and biophysical mechanisms of chromosome folding and insight into the role of the 4D nucleome in genome function, and particularly in establishing and maintaining cellular states in development and their loss in aging and disease To address these challenges, we have assembled a highly interdisciplinary Center with the goal of generating comprehensive 4D nucleome maps that represent the spatial, physical, dynamic and functional organization of the human genome during key transitions of the 4D nucleome during early and late stages in life. Our Center has extensive experience and produced 4DN Reference Hi-C and Micro-C Interaction maps, and FISH datasets to compare to Hi-C data. We have benchmarked technologies for mapping genome folding, and developed data standards, common file formats, Hi-C/Micro-C data processing and data visualization pipelines, and polymer simulation approaches. We also developed new methods to quantify the forces that drive chromosome folding (liquid chromatin Hi-C), to map loci at the nuclear periphery (Protect-seq), to detect topological catenations (multi-contact 3C) and to map sub-nuclear proteomes and transcriptomes (C-BERST). With a comprehensive suite of benchmarked genomic, imaging, proteomic assays and modeling tools now in hand, we will apply these approaches, and integrate and model the resulting data to determine pathways of how 4D nucleome develops during life span: from an immature state in embryonic stem cells, to a mature state during cell differentiation into hepatocytes, and then how the 4D nucleome changes again and deteriorates as cells (prematurely) age. We will map the 3D structure of the genome and associated proteins and RNAs, map loci near sub-nuclear structures, identify cell-to-cell variation in organization, quantify dynamic and biophysical properties of chromatin interactions, and relate chromosome and nuclear organization to gene expression. These different datatypes will be integrated to determine dynamic trajectories of the 4DN nucleome at the resolution of single loci as cells differentiate and age. Mechanistic models for chromosome folding will be formulated and experimentally tested. Finally, we will develop new platforms to visualize and widely share navigable maps of the dynamic 4D nucleome and 4D nucleome trajectories during cellular transitions.