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Multi-scale structural community organisation of the human genome

hal.structure.identifierUNICANCER - Institut régional du Cancer Montpellier Val d'Aurelle [ICM]
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorBOULOS, Rasha E.
hal.structure.identifierGIPSA - Communication Information and Complex Systems [GIPSA-CICS]
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorTREMBLAY, Nicolas
hal.structure.identifierLaboratoire Ondes et Matière d'Aquitaine [LOMA]
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorARNEODO, Alain
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorBORGNAT, Pierre
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorAUDIT, Benjamin
dc.date.created2016-08-23
dc.date.issued2017
dc.identifier.issn1471-2105
dc.description.abstractEnBackground: Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. Results: We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines. We observed that there exist structural domains of all sizes up to chromosome length and demonstrated that the set of structural communities forms a hierarchy of chromosome segments. Hence, at all scales, chromosome folding predominantly involves interactions between neighbouring sites rather than the formation of links between distant loci. Conclusions: Multi-scale structural decomposition of human chromosomes provides an original framework to question structural organisation and its relationship to functional regulation across the scales. By construction the proposed methodology is independent of the precise assembly of the reference genome and is thus directly applicable to genomes whose assembly is not fully determined.
dc.description.sponsorshipTraitement de signaux sur graphes - ANR-14-CE27-0001
dc.language.isoen
dc.publisherBioMed Central
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enHuman genome
dc.subject.enChromosome interaction network
dc.subject.enMulti-scale community mining
dc.subject.enStructural domain hierarchical organisation
dc.subject.enSpectral graph wavelets
dc.title.enMulti-scale structural community organisation of the human genome
dc.typeArticle de revue
dc.identifier.doi10.1186/s12859-017-1616-x
dc.subject.halPhysique [physics]/Physique [physics]/Biophysique [physics.bio-ph]
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique humaine
bordeaux.journalBMC Bioinformatics
bordeaux.page209
bordeaux.volume18
bordeaux.issue1
bordeaux.peerReviewedoui
hal.identifierhal-01507455
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01507455v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=BMC%20Bioinformatics&rft.date=2017&rft.volume=18&rft.issue=1&rft.spage=209&rft.epage=209&rft.eissn=1471-2105&rft.issn=1471-2105&rft.au=BOULOS,%20Rasha%20E.&TREMBLAY,%20Nicolas&ARNEODO,%20Alain&BORGNAT,%20Pierre&AUDIT,%20Benjamin&rft.genre=article


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