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Impact of chromosome fusions on 3D genome organization and gene expression in budding yeast

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dc.contributor.author Di Stefano, Marco
dc.contributor.author Di Giovanni, Francesca, 1985-
dc.contributor.author Pozharskaia, Vasilia
dc.contributor.author Gomar-Alba, Mercè
dc.contributor.author Baù, Davide
dc.contributor.author Carey, Lucas, 1980-
dc.contributor.author Marti-Renom, Marc A.
dc.contributor.author Mendoza, Manuel (Mendoza Palomares)
dc.date.accessioned 2020-03-23T10:53:50Z
dc.date.available 2020-03-23T10:53:50Z
dc.date.issued 2020
dc.identifier.citation Di Stefano M, Di Giovanni F, Pozharskaia V, Gomar-Alba M, Baù D, Carey LB. Impact of chromosome fusions on 3D genome organization and gene expression in budding yeast. Genetics. 2020 Mar; 214(3) :651-667. DOI: 10.1534/genetics.119.302978
dc.identifier.issn 0016-6731
dc.identifier.uri http://hdl.handle.net/10230/43995
dc.description.abstract The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.
dc.description.sponsorship This project was supported by European Research Council Starting grant 2010-St-20091118 and Spanish Ministry of Economy and Competitiveness grant BFU2012-37162 to M.M., and grant ANR-10-LABX-0030-INRT, which is a French State fund managed by the Agence Nationale de la Recherche under the frame Programme Investissements d’Avenir ANR-10-IDEX-0002-02 to the Institut de Génétique et de Biologie Moléculaire et Cellulaire. L.B.C. was supported by the Agència de Gestió d’Ajuts Universitaris i de Recerca (grant 2014 SGR 0974), and the Spanish Ministerio de Economía y Competitividad and the European Regional Development Fund (FEDER) (grant BFU2015-68351-P). M.A.M.-R. was supported by the European Union’s Horizon 2020 research and innovation programme (grant agreement 676556) and the Spanish Ministry of Economy and Competitiveness (grant BFU2017-85926-P). We also acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement and the Co-financing by Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program to the CRG. M.G.-A. is a recipient of a Postdoctoral Fellowship (APOSTD/2017/094) from the Generalitat Valenciana
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Genetics Society of America
dc.relation.ispartof Genetics. 2020 Mar; 214(3) :651-67
dc.rights © 2020 Marco Di Stefano et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Cromosomes
dc.subject.other Genomes
dc.subject.other Expressió gènica
dc.subject.other Llevats
dc.title Impact of chromosome fusions on 3D genome organization and gene expression in budding yeast
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1534/genetics.119.302978
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676556
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2012-37162
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-68351-P
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-85926-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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