2022
Biophysical Journal

Differences in nanoscale organization of regulatory active and inactive human chromatin

Authors:

Brandstetter, K., Zülske, T., Ragoczy, T., Hörl, D., Guirao-Ortiz, M., Steinek, C., ... & Harz, H.

Abstract:

Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. Analyzing genome-wide data from 733 human cell and tissue samples, we identified two prototypical regions that exhibit high or absent hypersensitivity to deoxyribonuclease I, respectively. These regulatory active or inactive regions were examined in the lymphoblast cell line K562 by using high throughput super-resolution microscopy. In both regions we systematically measured the physical distance of two fluorescence in situ hybridisation spots spaced by only 5 kb of DNA. Unexpectedly the resulting distance distributions range from very compact to almost elongated configurations of more than 200 nm length for both the active and inactive regions. Monte Carlo simulations of a coarse-grained model of these chromatin regions based on published data of nucleosome occupancy in K562 cells were performed to understand underlying mechanisms. There was no parameter set for the simulation model that can explain the microscopically measured distance distributions. Obviously, the chromatin state given by strength of internucleosomal interaction, nucleosome occupancy or amount of histone H1 differs from cell to cell which sums up to the observed broad distance distributions. This large variability was not expected, especially in inactive regions. The results for the mechanisms for different distance distributions on this scale is important for the understanding of contacts mediating gene regulation. Microscopic measurements show that the inactive region investigated here is expected to be embedded in a more compact chromatin environment. Simulation results of this region require an increase in the strength of internucleosomal interactions. It can be speculated that the higher density of chromatin is caused by the increased internucleosomal interaction strength.