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Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

View ORCID ProfileD. Michieletto, View ORCID ProfileE. Orlandini, D. Marenduzzo
doi: https://doi.org/10.1101/135756
D. Michieletto
1SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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  • For correspondence: davide.michieletto@ed.ac.uk
E. Orlandini
2Dipartimento di Fisica e Astronomia and Sezione INFN, Universitá di Padova, Via Marzolo 8, Padova 35131, Italy
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D. Marenduzzo
1SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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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 “epigenetic solitons” 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 09, 2017.
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Epigenetic Transitions and Knotted Solitons in Stretched Chromatin
D. Michieletto, E. Orlandini, D. Marenduzzo
bioRxiv 135756; doi: https://doi.org/10.1101/135756
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Epigenetic Transitions and Knotted Solitons in Stretched Chromatin
D. Michieletto, E. Orlandini, D. Marenduzzo
bioRxiv 135756; doi: https://doi.org/10.1101/135756

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