Three-dimensional genome organization via triplex-forming RNAs
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- dc.contributor.author Farabella, Irene
- dc.contributor.author Di Stefano, Marco
- dc.contributor.author Soler-Vila, Paula
- dc.contributor.author Marti Marimon, Maria
- dc.contributor.author Marti-Renom, Marc A.
- dc.date.accessioned 2021-12-17T11:54:30Z
- dc.date.available 2021-12-17T11:54:30Z
- dc.date.issued 2021
- dc.description.abstract An increasing number of long noncoding RNAs (lncRNAs) have been proposed to act as nuclear organization factors during interphase. Direct RNA-DNA interactions can be achieved by the formation of triplex helix structures where a single-stranded RNA molecule hybridizes by complementarity into the major groove of double-stranded DNA. However, whether and how these direct RNA-DNA associations influence genome structure in interphase chromosomes remain poorly understood. Here we theorize that RNA organizes the genome in space via a triplex-forming mechanism. To test this theory, we apply a computational modeling approach of chromosomes that combines restraint-based modeling with polymer physics. Our models suggest that colocalization of triplex hotspots targeted by lncRNAs could contribute to large-scale chromosome compartmentalization cooperating, rather than competing, with architectural transcription factors such as CTCF.
- dc.description.sponsorship This work was supported by the European Research Council under the 7th Framework Program FP7/2007-2013 (ERC grant agreement no. 609989 to M.A.M.-R.) and the Spanish Ministerio de Ciencia, Innovación y Universidades through nos. IJCI-2015-23352 to I.F. and BFU2017-85926-P and PID2020-115696RB-I00 to M.A.M.-R. CRG acknowledges support from ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 and the CERCA Program/Generalitat de Catalunya, as well as support from the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the EMBL partnership, the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement, and cofinancing with funds from the European Regional Development Fund by the Spanish Ministry of Science and Innovation corresponding to the Programa Opertaivo FEDER Plurirregional de España 2014–2020 and by the Secretaria d’Universitats i Recerca, Departament d’Empresa i Coneixement of the Generalitat de Catalunya corresponding to the program Operatiu FEDER Catalunya 2014–2020 and the NIH (to C.T. Wu no. R01HD091797 for supporting I.F.)
- dc.format.mimetype application/pdf
- dc.identifier.citation Farabella I, Di Stefano M, Soler-Vila P, Marti-Marimon M, Marti-Renom MA. Three-dimensional genome organization via triplex-forming RNAs. Nat Struct Mol Biol. 2021 Nov;28(11):945-954. DOI: 10.1038/s41594-021-00678-3
- dc.identifier.doi http://dx.doi.org/10.1038/s41594-021-00678-3
- dc.identifier.issn 1545-9993
- dc.identifier.uri http://hdl.handle.net/10230/49245
- dc.language.iso eng
- dc.publisher Nature Research
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/609989
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-85926-P
- dc.rights © Irene Farabella et al., under exclusive licence to Springer Nature America, Inc. 2021
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.subject.other Genètica
- dc.subject.other Genòmica
- dc.subject.other RNA
- dc.title Three-dimensional genome organization via triplex-forming RNAs
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/acceptedVersion