Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization

Simple item page
buir.contributor.authorErbaş, Aykut
buir.contributor.orcidErbaş, Aykut|0000-0003-2192-8804
dc.citation.epage056004-8en_US
dc.citation.issueNumber5
dc.citation.spage056004-1
dc.citation.volumeNumber20
dc.contributor.authorPaturej, J.
dc.contributor.authorErbaş, Aykut
dc.date.accessioned2024-03-13T07:33:14Z
dc.date.available2024-03-13T07:33:14Z
dc.date.issued2023-07-26
dc.departmentInstitute of Materials Science and Nanotechnology (UNAM)
dc.description.abstractInterphase chromosomes are known to organize non-randomly in the micron-sized eukaryotic cell nucleus and occupy certain fraction of nuclear volume, often without mixing. Using extensive coarse-grained simulations, we model such chromosome structures as colloidal particles whose surfaces are grafted by cyclic polymers. This model system is known as Rosetta. The cyclic polymers, with varying polymerization degrees, mimic chromatin loops present in interphase chromosomes, while the rigid core models the chromocenter section of the chromosome. Our simulations show that the colloidal chromosome model provides a well-separated particle distribution without specific attraction between the chain monomers. As the polymerization degree of the grafted cyclic chains decreases while maintaining the total chromosomal length (e.g. the more potent activity of condensin-family proteins), the average chromosomal volume becomes smaller, inter-chromosomal contacts decrease, and chromocenters organize in a quasi-crystalline order reminiscent of a glassy state. This order weakens for polymer chains with a characteristic size on the order of the confinement radius. Notably, linear-polymer grafted particles also provide the same chromocenter organization scheme. However, unlike linear chains, cyclic chains result in less contact between the polymer layers of neighboring chromosome particles, demonstrating the effect of DNA breaks in altering genome-wide contacts. Our simulations show that polymer-grafted colloidal systems could help decipher 3D genome architecture along with the fractal globular and loop-extrusion models.
dc.identifier.doi10.1088/1478-3975/ace750
dc.identifier.eissn1478-3975
dc.identifier.issn1478-3967
dc.identifier.urihttps://hdl.handle.net/11693/114654
dc.language.isoen
dc.publisherInstitute of Physics Publishing Ltd.
dc.relation.isversionofhttps://dx.doi.org/10.1088/1478-3975/ace750
dc.rightsCC BY 4.0 DEED (Attribution 4.0 International)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.source.titlePhysical Biology
dc.subjectChromosome organization
dc.subjectColloidal particles
dc.subjectCyclic polymers
dc.subjectMolecular simulations
dc.titleCyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization
dc.typeArticle

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Cyclic_polymer_grafted_colloids_in_spherical_confinement_insights_for_interphase_chromosome_organization.pdf
Size:
1.71 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
2.01 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

Institute of Materials Science and Nanotechnology (UNAM)