Comperhensive Characterization of Active and Inactive Chromatin in Human Cells by Superresolution Microscopy and Computer Simulations

Abstract

In chromatin DNA is wrapped around histone proteins forming so-called nucleosomes. These are the basic building blocks that organizes the DNA packaging. The nucleosome chain folds into a structure termed chromatin and is distinguished into active DNA comprising euchromatin and inactive DNA comprising heterochromatin. To better understand the underlaying processes and dynamics of these structures, two 5 kb regions (active, inactive) on chromosom 11 of the human genome were chosen by our collaboration partners in Munich. For these regions end to end measurements were executed repeatedly with the help of 3D STED microscopy. To verify the experimental data, our coarse-grained computer simulation model of chromatin was consolidated. In these nucleosomes are modelled as spherocylinders connected by elastic segments describing linker DNA. Interactions include stretching, bending, torsion, electrostatic and internucleosomal interactions. Configurations are sampled applying Metropolis Monte Carlo and replica exchange algorithms. One of the Results is indicating that an active region has different nucleosome occupancies in different cells. For this purpose, we first simulate the full nucleosome occupied active region and decreased the number of nucleosomes by one and simulate it again until 5 nucleosomes were deleted. After that, the end to end (Euclidean distance) distances of the lowest Temperature were measured and compared with the experimental histograms. The most interesting fact is that the addition of all histograms leads to a result which is much closer to the experimental one.