RT Journal Article
SR Electronic
T1 Differences in nanoscale organization of DNase I hypersensitive and insensitive chromatin in single human cells
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.05.27.445943
DO 10.1101/2021.05.27.445943
A1 Katharina Brandstetter
A1 Tilo Zülske
A1 Tobias Ragoczy
A1 David Hörl
A1 Eric Haugen
A1 Eric Rynes
A1 John A. Stamatoyannopoulos
A1 Heinrich Leonhardt
A1 Gero Wedemann
A1 Hartmann Harz
YR 2021
UL http://biorxiv.org/content/early/2021/05/27/2021.05.27.445943.abstract
AB 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. By using a combination of high throughput super-resolution microscopy and coarse-grained modelling we investigated properties of active and inactive chromatin in interphase nuclei. Using DNase I hypersensitivity as a criterion, we have selected prototypic active and inactive regions from ENCODE data that are representative for K-562 and more than 150 other cell types. By using oligoFISH and automated STED microscopy we systematically measured physical distances of the endpoints of 5kb DNA segments in these regions. These measurements result in high-resolution distance distributions which are right-tailed and range from very compact to almost elongated configurations of more than 200 nm length for both the active and inactive regions. Coarse-grained modeling of the respective DNA segments suggests that in regions with high DNase I hypersensitivity cell-to-cell differences in nucleosome occupancy determine the histogram shape. Simulations of the inactive region cannot sufficiently describe the compaction measured by microscopy, although internucleosomal interactions were elevated and the linker histone H1 was included in the model. These findings hint at further organizational mechanisms while the microscopy-based distance distribution indicates high cell-to-cell differences also in inactive chromatin regions. The analysis of the distance distributions suggests that direct enhancer-promoter contacts, which most models of enhancer action assume, happen for proximal regulatory elements in a probabilistic manner due to chromatin flexibility.Competing Interest StatementThe authors have declared no competing interest.