Browsing by Author "Rao, Suhas S.P."
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Item Cohesin depleted cells rebuild functional nuclear compartments after endomitosis(Springer Nature, 2020) Cremer, Marion; Brandstetter, Katharina; Maiser, Andreas; Rao, Suhas S.P.; Schmid, Volker J.; Guirao-Ortiz, Miguel; Mitra, Namita; Mamberti, Stefania; Klein, Kyle N.; Gilbert, David M.; Leonhardt, Heinrich; Cardoso, M. Cristina; Aiden, Erez Lieberman; Harz, Hartmann; Cremer, ThomasCohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture, linked to nuclear functions, is less well understood. Using live-cell and super-resolved 3D microscopy, here we find that cohesin depletion in a human colon cancer derived cell line results in endomitosis and a single multilobulated nucleus with chromosome territories pervaded by interchromatin channels. Chromosome territories contain chromatin domain clusters with a zonal organization of repressed chromatin domains in the interior and transcriptionally competent domains located at the periphery. These clusters form microscopically defined, active and inactive compartments, which likely correspond to A/B compartments, which are detected with ensemble Hi-C. Splicing speckles are observed nearby within the lining channel system. We further observe that the multilobulated nuclei, despite continuous absence of cohesin, pass through S-phase with typical spatio-temporal patterns of replication domains. Evidence for structural changes of these domains compared to controls suggests that cohesin is required for their full integrity.Item Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling(Public Library of Science, 2018) Nir, Guy; Farabella, Irene; Estrada, Cynthia Pérez; Ebeling, Carl G.; Beliveau, Brian J.; Sasaki, Hiroshi M.; Lee, S. Dean; Nguyen, Son C.; McCole, Ruth B.; Chattoraj, Shyamtanu; Erceg, Jelena; Abed, Jumana AlHaj; Martins, Nuno M.C.; Nguyen, Huy Q.; Hannan, Mohammed A.; Russell, Sheikh; Durand, Neva C.; Rao, Suhas S.P.; Kishi, Jocelyn Y.; Soler-Vila, Paula; Pierro, Michele Di; Onuchic, José N.; Callahan, Steven P.; Schreiner, John M.; Stuckey, Jeff A.; Yin, Peng; Aiden, Erez Lieberman; Marti-Renom, Marc A.; Wu, C.-tingChromosome organization is crucial for genome function. 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. 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. 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. 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. 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.