**2. Finalizing the 3D Genome Architecture & Dynamics**

Heuristically, it is very instructive how the central part of the 3D genome architecture and dynamics could now be determined by us in detail, and how out of this process immediately an also evolutionary consistent model (**Figure 1**) arises in agreement with the entire history and heuristics of the field. This has been achieved by a highly integrated systems approach linking holistically: i) a novel high-quality selective high-throughput high-resolution chromosome interaction capture (T2C) technique [25, 26, 67–69] (elucidating the structure with unprecedented resolution of some base pairs), ii) a novel *in vivo* FCS approach [27] exploring the structure and dynamics by measuring chromatin movement, and iii) a novel analytical approach [27] and improvement of super-computer simulations of individual chromosomes and entire cell nuclei [7, 21–24, 26, 49–52, 70] to predict, analyse, and interpret the 3D architecture and dynamics from a theoretical standpoint, and combining all these with iv) scaling analysis of the 3D-architecture [21, 22, 26] and the DNA sequence itself [22, 24, 26] since the architecture and its dynamics leaves sequence "footprints" due to the co-evolutionary entanglement of structure and sequence. The combination of these resulted not only in a consistent model for genome organization, but re-evaluation of the development of the entire field in the last ~170 years fostered this conclusion also tremendously and directly resulted in an

A Consistent Systems Mechanics Model of the 3D Architecture and Dynamics of Genomes

http://dx.doi.org/10.5772/intechopen.89836

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To finally determine and structurally sequence with highest resolution, signal-to-noise ratio, interaction frequency range, and statistical significance the 3D genome architecture we developed targeted chromatin capture (T2C) - a chromatin interaction technique though with far-better quality specifically addressing the needs for genome architectural "sequencing" [25, 26 67–69]. Briefly: i) after chromatin crosslinking, ii) cell permeabilization for intra-nuclear enzymatic DNA restriction, iii) the extracted and largely diluted cross-linked DNA is re-ligated primarily within the crosslinked complexes. After iv) decrosslinking, purification, and final shortening to <500 bp of the chimeric DNA ligates, v) a purified region-specific DNA interaction fragment library is selected by using DNA capture arrays, before finally vi) high-throughput sequencing, mapping to the reference genome, interaction partner determination and visual/quantitative analysis is conducted (**Figure 2**). Notably, we use only uniquely mapped sequences without applying any other corrections

c

**Figure 2.** Simulated chromosome models [7, 21–23, 26, 49–52]: Volume rendered images of simulated Random-Walk/ Giant-Loop (RW/GL) and Multi-Loop-Subcompartment (MLS) models. As a starting conformation with metaphase chromosome form and size (top), rosettes were stacked (a). Thereof, interphase chromosomes in thermodynamic equilibrium, were decondensed by Monte-Carlo and relaxing Brownian Dynamics. The simulated RW/GL model containing here large 5 Mbp loops notably shows that the large loops do not form distinct structures but intermingle freely (b). In contrast, in the MLS model with 126 kbp loops and linkers, the rosettes form distinct subchromosomal domains and chromatin territories in which the loops do not intermingle freely (c). In an RW/GL model with 126 kbp loops and 63 kbp linkers, again distinct chromatin territories are formed but in contrast to the MLS model without subchromosomal domains (d). It is obvious that the MLS model not only balances stability and flexibility considerations in storage and transcriptional respects, but also is optimal for replication due to its in essence two-dimensional topology

d

evolutionary consistent model of genome organization in general.

a

b

allowing controlled duplication and separation during mitosis.

**2.1. Detailed Structure Determination by T2C**

**Figure 1.** Overview on the size and time scaling of genome organization: The scaling and the levels of organization range over 9, 12, and 14 orders of magnitude! Initially base pairs are formed composing the DNA double helix (image see [22]), forming with a histone core complex the nucleosome (image from [22]), which condense into a chromatin quasi-fibre (simulation image; courtesy G. Wedemann). The DNA double helix forms also superhelices (AFM image of plasmid DNA; courtesy K. Rippe). The next compaction step consists of stable chromatin loops (FISH image; courtesy P. Fransz) forming stable loop aggregates/rosettes connected by a linker (EM image from [44]), which make up interphase chromosome arms and territories (FISH image; courtesy S. Dietzel) and the metaphase ideogram bands (image see [22]). 46 chromosomes compose the human nucleus and are decondensed in interphase (EM image; courtesy K. Richter) and condensed for separation during mitosis (image from [22]).

model for genome organization, but re-evaluation of the development of the entire field in the last ~170 years fostered this conclusion also tremendously and directly resulted in an evolutionary consistent model of genome organization in general.
