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• W2170647411 abstract "markdownabstractDespite the succesful linear sequencing of the human genome the three-dimensional arrangement of chromatin,functional, and structural components is still largely unknown. Molecular transport and diffusion are importantfor processes like gene regulation, replication, or repair and are vitally influenced by the structure. With acomparison between fluorescence correlation spectroscopy (FCS) experiments and simulations we show here aninterdisciplinary approach for the understanding of transport and diffusion properties in the human interphasecell nucleus. For a long time the interphase nucleus has been viewed as a 'spaghetti soup' of DNA without much internalstructure, except during cell division. Only recently has it become apparent that chromosomes occupy distinct'territories' also in interphase. Two models for the detailed folding of the 30 nm chromatin fibre within theseterritories are under debate: In the Random-Walk/Giant-Loop-model big loops of 3 to 5 Mbp are attached to anon-DNA backbone. In the Multi-Loop-Subcompartment (MLS) model loops of around 120 kbp are formingrosettes which are also interconnected by the chromatin fibre. Here we show with a comparison betweensimulations and experiments an interdisciplinary approach leading to a determination of the three-dimensionalorganization of the human genome: For the predictions of experiments various models of human interphasechromosomes and the whole cell nucleus were simulated with Monte Carlo and Brownian Dynamics methods.Only the MLS-model leads to the formation of non-overlapping chromosome territories and distinct functionaland dynamic subcompartments in agreement with experiments. Fluorescence in situ hybridization is used for thespecific marking of chromosome arms and pairs of small chromosomal DNA regions. The labelling is visualizedwith confocal laser scanning microscopy followed by image reconstruction procedures. Chromosome arms showonly small overlap and globular substructures as predicted by the MLS-model. The spatial distances betweenpairs of genomic markers as function of their genomic separation result in a MLS-model with loop and linkersizes around 126 kbp. With the development of GFP-fusion-proteins it is possible to study the chromatindistribution and dynamics resulting from cell cycle, treatment by chemicals or radiation in vivo. The chromatindistributions are similar to those found in the simulation of whole cell nuclei of the MLS-model. Fractal analysisis especially suited to quantify the unordered and non-euclidean chromatin distribution of the nucleus. Thedynamic behaviour of the chromatin structure and the diffusion of particles in the nucleus are also closelyconnected to the fractal dimension. Fractal analysis of the simulations reveal the multi-fractality ofchromosomes. First fractal analysis of chromatin distributions in vivo result in significant differences fordifferent morphologies and might favour a MLS-model-like chromatin distribution. Simulations of fragmentdistributions based on double strand breakage after carbon-ion irradiation differ in different models. Here again acomparison with experiments favours a MLS-model. FCS in combination with a scanning device is a suitable tool to study the diffusion characteristics of fluorescentproteins in living cell nuclei with high spatial resolution. Computer simulations of the three-dimensionalorganization of the human interphase nucleus allows a detailed test of theoretical models in comparison toexperiments. Diffusion and transport in the nucleus are most appropriately described with the concept ofobstructed diffusion. A large volume fraction of the nucleus seems to contain a cytosol-like liquid with anapparent viscosity 5 times higher than in water. The geometry of particles and structure as well as theirinteractions influence the mobilities in terms of speed and spatial coverage. A considerable amount of genomicsites is accessible for not too large particles. FCS experiments and simulations based on the polymer model arein a good agreement. Using recently developed in vivo chromatin markers, a detailed study of mobility vs.structure is subject of current work." @default.
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• W2170647411 date "2001-01-14" @default.
• W2170647411 modified "2023-09-27" @default.
• W2170647411 title "Diffusion and transport in the human interphase cell nucleus - FCS experiments compared to simulations." @default.
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