In our research, we used computer simulations to study the 3D organization of chromatin in the cell nucleus. This organization is fundamental to many aspects of cell biology. In the cover image of the April 2 issue of Biophysical Journal, we visualized chromatin at intermediate density with nucleosomes randomly spaced along the DNA, filling the space irregularly.

Chromatin consists of DNA wrapped around histone proteins, forming nucleosomes in a bead-on-string like manner. We simulated long chromatin chains packed in confined volumes. The image shows DNA, represented by a blue double helix, bound to histone octamer proteins, depicted as red cylinders. Our students Leif-Kristof Schultz and Frederic Bauer used our Chromatin 3D Visualizer (https://gitlab.com/wedemann-group/chromatin3d-visualizer) to visualize data from Monte Carlo simulations. Graphics Library Transmission Format data from this visualization was rendered by using Blender 3D computer graphics software to create the image. The double helix was interpolated from the coarse-grained segments that describe it.

The article suggests that the regular spacing of nucleosomes along DNA can result in more regular spatial structures, which can affect the accessibility of chromatin to diffusive factors such as transcription factors Density has only a small effect on structure and accessibility. These findings underscore the importance of nucleosome positions in controlling genomic activity.

You can find more information on our work at https://bioinformatics.hochschule-stralsund.de/ and https://www.bioimaging.bio.lmu.de/research/research-group-leonhardt/index.html.

— Tilo Zülske, Aymen Attou, Laurens Groß, David Hörl, Hartmann Harz, and Gero Wedemann