Targeted Chromatin Capture (T2C): A novel high resolution high throughput method to detect genomic interactions and regulatory elements.

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 of concentrated research, one of the central issues of our time. With a systems genomics combination of T2C and FCS together with analytical and simulated polymer models as well as scaling analysis of the architecture and the DNA sequence itself, we determined the architecture and dynamics with with molecular resolution from the single base to the mega base pair level! T2C is a novel superior selective high-throughput high-resolution chromosomal interaction capture of all physical genomic interactions (T2C) which has great advantages since it allows to reach an optimal combination of resolution, interaction frequency range, and multi-plexability, at unprecidented signal-to-noise ratio of multiple orders of magnitude. Actually, with T2C the ultimate limits at the level of the “genomic uncertainty principle” and “genomic statistical mechanics”, is reached. In parallel, with a novel FCS approach it is possible to determine the relaxation of local concentration fluctuations of the chromatin fibre and derive based on an analytical polymer model the relation between average persistence length, mass density and chromatin architecture. Whereas T2C measures architectural parameters, the FCS approach allows to measure in vivo the dynamics of the architecture. As common ground polymer simulations using Monte Carlo and Brownian Dynamics approaches as well as scaling analysis of the architecture as well as the DNA sequence organization itself round-off the experimental techniques in detail. In combination all four approaches reach agreement concerning the 3D architecture and dynamics of genomes in detail. With this we investigated several loci in detail of different species, cell type, and functional states from some to the mega-base pair level and thus spanning 6 orders of magnitude (!), and finally determined the three-dimensional organization and dynamics for the first time in a consisten system genomics manner from the four mentioned angles. Beyond, the results are also in agreement with the heuristics of the research of the last 170 years. Consequently, we have not only finally determined the architecture and dynamics of the mouse and human genome with base pair/molecular resolution, but this also opens now the detailed architectural and dynamic sequencing of genomes in a systems genomic manner which is of fundamental importance from fundamental genome understanding to diagnosis and treatment.