@article {Michieletto135756, author = {D. Michieletto and E. Orlandini and D. Marenduzzo}, title = {Epigenetic Transitions and Knotted Solitons in Stretched Chromatin}, elocation-id = {135756}, year = {2017}, doi = {10.1101/135756}, publisher = {Cold Spring Harbor Laboratory}, abstract = {The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to {\textquotedblleft}epigenetic solitons{\textquotedblright} which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.}, URL = {https://www.biorxiv.org/content/early/2017/05/09/135756}, eprint = {https://www.biorxiv.org/content/early/2017/05/09/135756.full.pdf}, journal = {bioRxiv} }