Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Friday Speaker Abstracts

MESOSCALE BOTTOM-UP APPROACH TO THE STUDY OF CHROMATIN TOPOLOGICAL CONFORMATIONS: FROM THE NUCLEOSOME TO 1MBP Artemi Bendandi 1,2 ; Aymeric Le Gratiet 2 ; Silvia Dante 2 ; Walter Rocchia 3 ; Alberto Diaspro 1,2 ; 1 University of Genoa, Physics, Genoa, Genova, Italy 2 IIT Genova, Nanoscopy & NIC@IIT, Genoa, Genova, Italy 3 IIT Genova, CONCEPT Lab, Genoa, Genova, Italy Understanding the mechanistic details underlying DNA compaction is key to the study of biological processes. While the first level of compaction, the nucleosome, has been studied in atomic resolution, the topology of the chromatin fibre remains debated. Therefore, there is a growing need for studies featuring a synergy between theoretical and experimental approaches, and the cross-validation of respective results. We propose a mesoscale bottom-up model: starting from the all-atom human nucleosome crystal structure, we move on to a coarse-grained approach where nucleosomes and linker DNA are each represented as three interacting centres. We parameterise our model with all-atom Molecular Dynamics (MD) and energetic estimates from the non-linear Poisson-Boltzmann equation. Starting from a map of nucleosome core particle (NCP) and linker DNA energy conformations varying relative position and orientation, we perform all-atom MD simulations on NCPs, linker DNA, and NCP with linker DNA. In our mesoscale force-field we consider three main kinds of interaction: mechanical, desolvation and electrostatic. This simplified model allows the study of larger conformations of the chromatin fibre, beyond the oligonucleosome level. We perform accompanying and complementary experiments, focusing on non-invasive methods that do not require aggressive sample preparation that could perturb the topology: Differential Scanning Calorimetry, Atomic Force Microscopy, Mueller Matrix Microscopy and, in future, Small Angle X-Ray Scattering. Our experiments will explore conformational states and changes depending on variations of parameters such as monovalent ion concentration, NCP number, and temperature. We validate intermediate results comparing them to existing oligonucleosome models in literature and to our own experiments, aimed at providing structural and thermodynamical information. Overall, we propose a cohesive mesoscale bottom-up model, combining simulations and experiments, thus testing different hypotheses in order to shed light on the determinants of chromatin conformation.

29