A systems genomic approach combining simulations and experiments reveals the detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of genomes.

The dynamic three-dimensional chromatin architecture of genomes and the obvious co-evolutionary connection to its function – the storage and expression of genetic information – is still debated after ~170 years of research. With a systems genomics approach combining quantitative polymer super-computer simulations, analytical models, and scaling analysis of both architecture and DNA sequence, with experimentally novel selective high-throughput chromosomal interaction capture (T2C) and novel in vivo 2D fluorescence correlation spectroscopy (2D-FCS) techniques, we determined and cross-proved finally the architecture of genomes with unprecedented molecular resolution and dynamic range from single base pairs to entire chromosomes: for several genetic loci of different species, cell type, cell cycle, and functional states a chromatin quasi-fibre exists with 5±1 nucleosome per 11 nm, which folds into stable(!) 40-100 kbp loops forming stable(!) aggregates/rosettes which are connected by a ~50 kbp chromatin linker. A priori, Monte Carlo and Brownian Dynamics methods were used to simulate the Multi-Loop-Subcompartment (MLS) model, in which ~100 kbp loops form rosettes, connected by a linker, and the Random-Walk/Giant-Loop (RW/GL) topology, in which 1-5 Mbp loops are attached to a flexible backbone. Both the MLS and the RW/GL model form chromosome territories but only the MLS rosettes result in distinct subcompartments visible with light microscopy and low overlap of chromosomes, -arms and subcompartments. The MLS morphology, the size of subcompartments and chromatin density distribution of simulated confocal (CLSM) images agree with the expression of fusionproteins from the histones with the autofluorescent proteins which also revealed different interphase morphologies for different cell lines. Even small changes of the model parameters induced significant rearrangements of the chromatin morphology. Thus, pathological diagnoses are closely related to structural changes on the chromatin level. Review and comparison of experimental to simulated spatial distance measurements between genomic markers as function of their genomic separation, as well as DNA fragment distributions after ion-irradiation also favour the above mentioned architecture and dynamics. Most importantly experiments with newly developed T2C and in vivo 2D-FCS techniques proof all this independently and allow the exact quantitative determination of parameters with unprecedented resolution. Finally, we find a fine-structured multi-scaling behaviour of both the simulated and experimentally determined architecture and the DNA sequence, showing for the first time directly the tight entanglement between architecture and DNA sequence. The found organization has fundamental consequences for the entire system of the storage and expression of genetic information as well as for its investigation: E.g. this architecture, its dynamics, and accessibility balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in-)active units already in proximity. Thus, our systems genomics approach opens the door to “architectural and dynamic sequencing” and “virtual systems simulation” of genomes at a resolution where a genome mechanics with corresponding uncertainty principles applies. Consequently, this will lead now to a detailed understanding of genomes with fundamental new insights and huge novel perspectives for diagnosis, treatment and genome engineering efforts in the future.