Here, we apply our strategy for tracing chromosomes at super-resolution, traversing over 8 megabases of human chromosome 19 while visualizing genomic features ranging in size from kilobases to megabases. In fact, studies of processes as diverse as gene activation and repression as well as genome repair and stability are all querying how the 3D organization of chromosomal DNA may be a major player. Questions regarding the impact of chromosome structure on genome function are focusing increasingly on the manner in which chromosomes are organized within the nucleus. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method– integrative modeling of genomic regions (IMGR)–to increase the genomic resolution of our traces to 10 kb. Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized.
Focusing on chromosomal regions that contribute to compartments, we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Chromosome organization is crucial for genome function.
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