In the nucleus of eukaryotic cells, DNA wraps around histone proteins to form nucleosomes, which in turn associate in a compact and dynamic fiber called chromatin. The physical properties of this fiber at different lengthscales, from the DNA double-helix to micrometer-sized chromosomes, are essential to the complex mechanisms of gene expression and its regulation. The present thesis is a contribution to the development of physical models, which are able to link different scales and to interpret and integrate data from a wide range of experimental and computational approaches. In the first part, we use Molecular Dynamics simulations of DNA oligomers to study doublehelical DNA at different temperatures. We estimate the sequence-dependent contribution of entropy to DNA elasticity, in relation with recent experiments on DNA persistence length. In the second part, we model the DNA-histone interactions within the nucleosome core particle,using DNA nanomechanics to extract a force field from a set of crystallographic nucleosome structures and Molecular Dynamics snapshots. In the third part, we consider the softer part of the nucleosome, the linker DNA between coreparticles which transiently associates with the histone H1 to form a "stem".We combine existing structural knowledge with experimental data at two different resolutions (DNA footprints and electro-micrographs) to develop a nanoscale model of the stem.
| Identifer | oai:union.ndltd.org:CCSD/oai:tel.archives-ouvertes.fr:tel-00756315 |
| Date | 28 September 2012 |
| Creators | Meyer, Sam |
| Publisher | Ecole normale supérieure de lyon - ENS LYON |
| Source Sets | CCSD theses-EN-ligne, France |
| Language | English |
| Detected Language | English |
| Type | PhD thesis |
Page generated in 0.0019 seconds