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- W2116920008 abstract "markdownabstractDespite the successful linear sequencing of the human genome its three-dimensional structure is widelyunknown, although it is important for gene regulation and replication. For a long time the interphase nucleus hasbeen viewed as a 'spaghetti soup' of DNA without much internal structure, except during cell division. Onlyrecently has it become apparent that chromosomes occupy distinct 'territories' also in interphase. Two models forthe detailed folding of the 30 nm chromatin fibre within these territories are under debate: In the Random-Walk/Giant-Loop-model big loops of 3 to 5 Mbp are attached to a non-DNA backbone. In the Multi-Loop-Subcompartment (MLS) model loops of around 120 kbp are forming rosettes which are also interconnected bythe chromatin fibre. Here we show with a comparison between simulations and experiments an interdisciplinaryapproach leading to a determination of the three-dimensional organization of the human genome: For the predictions of experiments various models of human interphase chromosomes and the whole cell nucleuswere simulated with Monte Carlo and Brownian Dynamics methods. Only the MLS-model leads to theformation of non-overlapping chromosome territories and distinct functional and dynamic subcompartments inagreement with experiments. Fluorescence in situ hybridization is used for the specific marking of chromosomearms and pairs of small chromosomal DNA regions. The labelling is visualized with confocal laser scanningmicroscopy followed by image reconstruction procedures. Chromosome arms show only small overlap andglobular substructures as predicted by the MLS-model. The spatial distances between pairs of genomic markersas function of their genomic separation result in a MLS-model with loop and linker sizes around 126 kbp. Withthe development of GFP-fusion-proteins it is possible to study the chromatin distribution and dynamics resultingfrom cell cycle, treatment by chemicals or radiation in vivo. The chromatin distributions are similar to thosefound in the simulation of whole cell nuclei of the MLS-model. Fractal analysis is especially suited to quantifythe unordered and non-euclidean chromatin distribution of the nucleus. The dynamic behaviour of the chromatinstructure and the diffusion of particles in the nucleus are also closely connected to the fractal dimension. Fractalanalysis of the simulations reveal the multi-fractality of chromosomes. First fractal analysis of chromatindistributions in vivo result in significant differences for different morphologies and might favour a MLS-modellikechromatin distribution. Simulations of fragment distributions based on double strand breakage after carbonionirradiation differ in different models. Here again a comparison with experiments favours a MLS-model." @default.
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- W2116920008 date "2000-10-19" @default.
- W2116920008 modified "2023-09-27" @default.
- W2116920008 title "Three-dimensional organization of the human interphase nucleus: Experiments compared to simulations." @default.
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