Approaching the Three-Dimensional Organization and Dynamics of the Human Genome

To approach the still largely unknown sequential and three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated on the 30nm chromatin fiber level with Monte Carlo, Brownian Dynamics and parallel computing methods. Differences between used models explain various experimental conditions, favouring a Multi-Loop-Subcompartment model with 63-126kbp loops aggregated to possibly rosettes connected by 63-126kbp linkers, and predict correctly the transport of molecules by moderately obstructed diffusion excluding the Inter-Chromosomal Domain hypothesis. Correlation analyses of completely sequenced Archaea, Bacteria and Eukarya chromosomes revealed fine-structured positive long-range correlations due to codon, nucleosomal or block organization of the genomes, allowing classification and tree construction. By construction and expression of fusion proteins from the histones H1, H2A, H2B, H3, H4 and mH2A1.2 with the auto-fluorescent proteins CFP, GFP, YFP, DsRed-1 and DsRed-2, the chromatin morphology could be investigated in vivo during interphase, mitosis or apoptosis and revealed different interphase morphologies for cell lines, quantifiable by scaling analyses. Finally, construct conversions in simultaneous co- transfections due to recombination/ repair/replication were discovered in ≤25% of cells and led to a variety of new applications.