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dc.contributor.authorZhu, Fangjie
dc.contributor.authorFarnung, Lucas
dc.contributor.authorKaasinen, Eevi
dc.contributor.authorSahu, Biswajyoti
dc.contributor.authorYin, Yimeng
dc.contributor.authorWei, Bei
dc.contributor.authorDodonova, Svetlana O
dc.contributor.authorNitta, Kazuhiro R
dc.contributor.authorMorgunova, Ekaterina
dc.contributor.authorTaipale, Minna
dc.contributor.authorCramer, Patrick
dc.contributor.authorTaipale, Anssi
dc.date.accessioned2018-09-21T15:21:11Z
dc.date.available2018-09-21T15:21:11Z
dc.date.issued2018-10
dc.identifier.issn1476-4687
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/280617
dc.description.abstractNucleosomes cover most of the genome and are thought to be displaced by transcription factors (TFs) in regions that direct gene expression. However, the modes of interaction between TFs and nucleosomal DNA remain largely unknown. Here, we have systematically explored interactions between the nucleosome and 220 TFs representing diverse structural families. Consistently with earlier observations, we find that the majority of the studied TFs have less access to nucleosomal DNA than to free DNA. The motifs recovered from TFs bound to nucleosomal and free DNA are generally similar; however, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many TFs preferentially bind close to the end of nucleosomal DNA, or to periodic positions at its solvent-exposed side. TFs often also bind to nucleosomal DNA in a particular orientation. Some TFs specifically interact with DNA located at the dyad position where only one DNA gyre is wound, whereas other TFs prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals striking differences in TF binding to free and nucleosomal DNA, and uncovers a rich interaction landscape between TFs and the nucleosome.
dc.publisherSpringer Nature
dc.titleThe interaction landscape between transcription factors and the nucleosome
dc.typeArticle
prism.endingPage81
prism.publicationNameNature
prism.startingPage76
prism.volume562
dc.identifier.doi10.17863/CAM.27983
dcterms.dateAccepted2018-08-06
rioxxterms.versionofrecord10.1038/s41586-018-0549-5
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2018-08-06
dc.contributor.orcidTaipale, Minna [0000-0002-1905-2551]
dc.contributor.orcidTaipale, Anssi [0000-0003-4204-0951]
dc.identifier.eissn1476-4687
rioxxterms.typeJournal Article/Review
cam.issuedOnline2018-09-24
rioxxterms.freetoread.startdate2019-03-24


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