Despite the successful linear sequencing of the human genome its three-dimensional structure is widely
unknown, although it is important for gene regulation and replication. For a long time the interphase nucleus has
been viewed as a 'spaghetti soup' of DNA without much internal structure, 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 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 by
the chromatin fibre. Here we show with a comparison between simulations and experiments an interdisciplinary
approach 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 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 functional and dynamic subcompartments in
agreement with experiments. Fluorescence in situ hybridization is used for the specific marking of chromosome
arms and pairs of small chromosomal DNA regions. The labelling is visualized with confocal laser scanning
microscopy followed by image reconstruction procedures. Chromosome arms show only small overlap and
globular substructures as predicted by the MLS-model. The spatial distances between pairs of genomic markers
as function of their genomic separation result in a MLS-model with loop and linker sizes around 126 kbp. With
the development of GFP-fusion-proteins it is possible to study the chromatin distribution and dynamics resulting
from cell cycle, treatment by chemicals or radiation in vivo. The chromatin distributions are similar to those
found in the simulation of whole cell nuclei of the MLS-model. Fractal analysis is especially suited to quantify
the unordered and non-euclidean chromatin distribution of the nucleus. The dynamic behaviour of the chromatin
structure and the diffusion of particles in the nucleus are also closely connected to the fractal dimension. Fractal
analysis of the simulations reveal the multi-fractality of chromosomes. First fractal analysis of chromatin
distributions in vivo result in significant differences for different morphologies and might favour a MLS-modellike
chromatin distribution. Simulations of fragment distributions based on double strand breakage after carbonion
irradiation differ in different models. Here again a comparison with experiments favours a MLS-model
