Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale
Interactions of chromatin with the nuclear lamina imposes a radial genome distribution important for nuclear functions. How physical properties of chromatin affect these interactions is unclear. We used polymer simulations to model how physical parameters of chromatin affect its interaction with the...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2021-01-01
|
| Series: | Nucleus |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/19491034.2020.1868105 |
| _version_ | 1818701218400174080 |
|---|---|
| author | Annaël Brunet Nicolas Destainville Philippe Collas |
| author_facet | Annaël Brunet Nicolas Destainville Philippe Collas |
| author_sort | Annaël Brunet |
| collection | DOAJ |
| description | Interactions of chromatin with the nuclear lamina imposes a radial genome distribution important for nuclear functions. How physical properties of chromatin affect these interactions is unclear. We used polymer simulations to model how physical parameters of chromatin affect its interaction with the lamina. Impact of polymer stiffness is greater than stretching on its configurations at the lamina; these are manifested as trains describing extended interactions, and loops describing desorbed regions . Conferring an attraction potential leads to persistent interaction and adsorption-desorption regimes manifested by fluctuations between trains and loops. These are modulated by polymer stiffness and stretching, with a dominant impact of stiffness on resulting structural configurations. We infer that flexible euchromatin is more prone to stochastic interactions with lamins than rigid heterochromatin characterizing constitutive LADs. Our models provide insights on the physical properties of chromatin as a polymer which affect the dynamics and patterns of interactions with the nuclear lamina. |
| first_indexed | 2024-12-17T15:17:21Z |
| format | Article |
| id | doaj.art-c016db72232f4af9aef7d0c0207de085 |
| institution | Directory Open Access Journal |
| issn | 1949-1034 1949-1042 |
| language | English |
| last_indexed | 2024-12-17T15:17:21Z |
| publishDate | 2021-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Nucleus |
| spelling | doaj.art-c016db72232f4af9aef7d0c0207de0852022-12-21T21:43:29ZengTaylor & Francis GroupNucleus1949-10341949-10422021-01-0112162010.1080/19491034.2020.18681051868105Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scaleAnnaël Brunet0Nicolas Destainville1Philippe Collas2Institute of Basic Medical Sciences, Faculty of Medicine, University of OsloLaboratoire De Physique Théorique, IRSAMC, Université De Toulouse (UPS)Institute of Basic Medical Sciences, Faculty of Medicine, University of OsloInteractions of chromatin with the nuclear lamina imposes a radial genome distribution important for nuclear functions. How physical properties of chromatin affect these interactions is unclear. We used polymer simulations to model how physical parameters of chromatin affect its interaction with the lamina. Impact of polymer stiffness is greater than stretching on its configurations at the lamina; these are manifested as trains describing extended interactions, and loops describing desorbed regions . Conferring an attraction potential leads to persistent interaction and adsorption-desorption regimes manifested by fluctuations between trains and loops. These are modulated by polymer stiffness and stretching, with a dominant impact of stiffness on resulting structural configurations. We infer that flexible euchromatin is more prone to stochastic interactions with lamins than rigid heterochromatin characterizing constitutive LADs. Our models provide insights on the physical properties of chromatin as a polymer which affect the dynamics and patterns of interactions with the nuclear lamina.http://dx.doi.org/10.1080/19491034.2020.1868105polymer modelingkinetic monte carlonuclear laminachromatinlamin-chromatin interaction |
| spellingShingle | Annaël Brunet Nicolas Destainville Philippe Collas Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale Nucleus polymer modeling kinetic monte carlo nuclear lamina chromatin lamin-chromatin interaction |
| title | Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale |
| title_full | Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale |
| title_fullStr | Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale |
| title_full_unstemmed | Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale |
| title_short | Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale |
| title_sort | physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale |
| topic | polymer modeling kinetic monte carlo nuclear lamina chromatin lamin-chromatin interaction |
| url | http://dx.doi.org/10.1080/19491034.2020.1868105 |
| work_keys_str_mv | AT annaelbrunet physicalconstraintsinpolymermodelingofchromatinassociationswiththenuclearperipheryatkilobasescale AT nicolasdestainville physicalconstraintsinpolymermodelingofchromatinassociationswiththenuclearperipheryatkilobasescale AT philippecollas physicalconstraintsinpolymermodelingofchromatinassociationswiththenuclearperipheryatkilobasescale |