Determination of the three-dimensional organization of chromatin by modelling-supported selective chromosomal interaction capture (T2C).

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, after ~170 years, a central question of current research. With a systems genomics approach using a novel selective high-throughput chromosomal interaction capture (T2C) technique together with quantitative polymer simulations and scaling analysis of genomic structures and the DNA sequence, we determined the architecture of genomes with unprecedented molecular resolution and dynamic range from single base pair entire chromosomes: for several genetic loci of different species, cell type, and functional states we find a chromatin quasi-fibre exists with 5±1 nucleosome per 11 nm, which folds into 40-100 kbp loops forming aggregates/rosettes which are connected by a ~50 kbp chromatin linker. Polymer simulations using Monte Carlo and Brownian dynamics approaches confirm T2C results and allow to predict and explain additional experimental findings. This agrees also with novel dynamics information from fluorescence correlation spectroscopy (FCS) analysis of chromatin relaxations in vivo (see abstract M. Wachsmuth & T. A. Knoch, Dynamic and structural properties of interphase chromatin mapped in vivo with fluorescence correlation spectroscopy and quantitative modelling). Beyond, we find a fine-structured multi-scaling behaveour of both the architecture and the DNA sequence which shows for the first time, that genome architecture and DNA sequence organiztion are directly linked – again in detail on the base pair level. Hence, we determined the three-dimensional organization and dynamics for the first time in a consistent system genomics manner from several angles which are all in agreement as well as additionally also with the heuristics of the research of the last 170 years. Consequently, T2C allows to reach an optimal combination of resolution, interaction frequency range, multi-plexing, and an unseen signal-to-noise ratio at molecular resolution and hence at the level of the “genomic” uncertainty principle and statistical mechanics, this opens the door to architectural sequencing of genomes and thus a detailed understanding of the genome with fundamental new insights with perspectives for diagnosis and treatment.