umu.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Mapping the spectrum of 3D communities in human chromosome conformation capture data
Show others and affiliations
2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 6859Article in journal (Refereed) Published
Abstract [en]

Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data show that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins-a loop-stabilizing protein that is ascribed a big role in TAD formation-are well correlated with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019. Vol. 9, article id 6859
National Category
Genetics
Identifiers
URN: urn:nbn:se:umu:diva-159053DOI: 10.1038/s41598-019-42212-yISI: 000466505500009PubMedID: 31048738OAI: oai:DiVA.org:umu-159053DiVA, id: diva2:1317108
Available from: 2019-05-21 Created: 2019-05-21 Last updated: 2019-05-21Bibliographically approved

Open Access in DiVA

fulltext(3609 kB)28 downloads
File information
File name FULLTEXT01.pdfFile size 3609 kBChecksum SHA-512
423c8774fd170dbbdeee69622b755144f1240cbdb9886a044ed41f5bf4e1f9872df84b4221147de904af34b1e4a93be4ec14bbc4b1fd0e41a0c23408d5ae21da
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records BETA

Stenberg, PerLizana, Ludvig

Search in DiVA

By author/editor
Stenberg, PerLizana, Ludvig
By organisation
Department of Ecology and Environmental SciencesDepartment of Physics
In the same journal
Scientific Reports
Genetics

Search outside of DiVA

GoogleGoogle Scholar
Total: 28 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 110 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf