Three-Dimensional Organization of Chromosome Territories in the Human Interphase Nucleus

Despite the successful linear sequencing of the human genome its three-dimensional structure is widely unknown. The regulation of genes has been shown to be connected closely to the three-dimensional organization of the genome in the cell nucleus. The nucleus of the cell has for a long time been viewed as a 'spaghetti soup' of DNA bound to various proteins without much internal structure, except during cell division, i.e. metaphase. Only recently has it become apparent that chromosomes occupy distinct 'territories' also in the interphase. In an analogy of the Bauhaus principle that "form follows function" we believe that analyzing in which form DNA is organized in these territories will help us to understand genomic function.We use computer models - Monte Carlo and Brownian dynamics simulations - to develop plausible proposals for the structure of the interphase genome. We simulate interphase chromosomes for different folding morphologies of the chromatin fiber which is organized into loops of 100 kbp to 3 Mbp that can be interconnected in various ways. The backbone of the fiber is described by a wormlike-chain polymer whose diameter and stiffness can be estimated from independent measurements. The implementation describes this polymer as a segmented chain with 3000 to 20000 segments for chromosome 15 depending on the phase of the simulation. The modeling is performed on parallel computers (IBM SP2 with 80 nodes, IBM SP2 with 512 nodes, Cray T3E). We also determine genomic marker distributions within the Prader-Willi-Region on chromosome 15q11.2-13.3. For these measurements we use a fluorescence in situ hybridization (FISH) method (in collaboration with I. Solovai and T. Cremer, Munich, FRG) conserving the structure of the nucleus. As probes we use 10 kbp long lambda clones (K. Büttig and Prof. B. Horsthemke, Essen, FRG) covering genomic marker distances between 8 kbp and 250 kbp. The markers are detected with confocal and standing wave-field light microscopes and using special image reconstruction methods developed for this purpose (in collaboration with J.Rauch, H. Bornfledth, C. Cremer, Heidelberg, FRG). Best agreement between simulations and experiments is reached for a Multi-Loop-Subcompartment model (126 kbp loops connected to rosettes connected by a 126 kbp chromatin linker). A fractal analysis of simulations leads to multi-fractal behaveour in good agreement with porous network research. The formation of chromosome territories was shown as predicted and low overlap of chromosomes and their arms was also reached in contrast to other models. Thus the human interphase cell nucleus shows a higher degree of determinism than previously thought.