Investigation of the Chromosome Regions with Significant Affinity for the Nuclear Envelope in Fruit Fly - A Model Based Approach

Simple item page
dc.contributor.authorKinney, Nicholas A.en
dc.contributor.authorSharakhov, Igor V.en
dc.contributor.authorOnufriev, Alexey V.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentEntomologyen
dc.contributor.departmentPhysicsen
dc.date.accessioned2017-01-05T23:42:56Zen
dc.date.available2017-01-05T23:42:56Zen
dc.date.issued2014-03-20en
dc.description.abstractThree dimensional nuclear architecture is important for genome function, but is still poorly understood. In particular, little is known about the role of the ‘‘boundary conditions’’ – points of attachment between chromosomes and the nuclear envelope. We describe a method for modeling the 3D organization of the interphase nucleus, and its application to analysis of chromosome-nuclear envelope (Chr-NE) attachments of polytene (giant) chromosomes in Drosophila melanogaster salivary glands. The model represents chromosomes as self-avoiding polymer chains confined within the nucleus; parameters of the model are taken directly from experiment, no fitting parameters are introduced. Methods are developed to objectively quantify chromosome territories and intertwining, which are discussed in the context of corresponding experimental observations. In particular, a mathematically rigorous definition of a territory based on convex hull is proposed. The self-avoiding polymer model is used to re-analyze previous experimental data; the analysis suggests 33 additional Chr-NE attachments in addition to the 15 already explored Chr-NE attachments. Most of these new Chr-NE attachments correspond to intercalary heterochromatin – gene poor, dark staining, late replicating regions of the genome; however, three correspond to euchromatin – gene rich, light staining, early replicating regions of the genome. The analysis also suggests 5 regions of anti-contact, characterized by aversion for the NE, only two of these correspond to euchromatin. This composition of chromatin suggests that heterochromatin may not be necessary or sufficient for the formation of a Chr- NE attachment. To the extent that the proposed model represents reality, the confinement of the polytene chromosomes in a spherical nucleus alone does not favor the positioning of specific chromosome regions at the NE as seen in experiment; consequently, the 15 experimentally known Chr-NE attachment positions do not appear to arise due to non-specific (entropic) forces. Robustness of the key conclusions to model assumptions is thoroughly checked.en
dc.description.versionPublished versionen
dc.format.extent? - ? (10) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1371/journal.pone.0091943en
dc.identifier.issn1932-6203en
dc.identifier.issue3en
dc.identifier.urihttp://hdl.handle.net/10919/73978en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherPLOSen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000333352800056&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectmelanogaster polytene chromosomesen
dc.subjectsalivary-gland nucleien
dc.subjectself-avoiding walksen
dc.subjectdrosophila-melanogasteren
dc.subjectinterphase chromosomesen
dc.subjectspatial-organizationen
dc.subjectin-vivoen
dc.subject3-dimensional organizationen
dc.subjectmammalian-cellsen
dc.subjectbudding yeasten
dc.titleInvestigation of the Chromosome Regions with Significant Affinity for the Nuclear Envelope in Fruit Fly - A Model Based Approachen
dc.title.serialPLOS ONEen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Entomologyen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach.pdf
Size:
634.57 KB
Format:
Adobe Portable Document Format
Description:
Publisher's Version
Download
License bundle
Now showing 1 - 1 of 1
Name:
VTUL_Distribution_License_2016_05_09.pdf
Size:
18.09 KB
Format:
Adobe Portable Document Format
Description:
Download

Collections

All Faculty Deposits
Scholarly Works, Computer Science
Scholarly Works, Entomology
Scholarly Works, Physics