Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Cattoni, Diego Ignacio; Cardozo Gizzi, Andrés M.; Georgieva, Mariya; Di Stefano, Marco; Valeri, Alessandro; Chamousset, Delphine; Houbron, Christophe; Déjardin, Stéphanie; Fiche, Jean Bernard; González, Inma Royo; Chang, Jia-Ming, 1978-; Sexton, Tom; Martí Renom, Marc A.; Bantignies, Frédéric; Cavalli, Giacomo; Nollmann, Marcelo

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

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dc.contributor.author Cattoni, Diego Ignacioca
dc.contributor.author Cardozo Gizzi, Andrés M.ca
dc.contributor.author Georgieva, Mariyaca
dc.contributor.author Di Stefano, Marcoca
dc.contributor.author Valeri, Alessandroca
dc.contributor.author Chamousset, Delphineca
dc.contributor.author Houbron, Christopheca
dc.contributor.author Déjardin, Stéphanieca
dc.contributor.author Fiche, Jean Bernardca
dc.contributor.author González, Inma Royoca
dc.contributor.author Chang, Jia-Ming, 1978-ca
dc.contributor.author Sexton, Tomca
dc.contributor.author Martí Renom, Marc A.ca
dc.contributor.author Bantignies, Frédéricca
dc.contributor.author Cavalli, Giacomoca
dc.contributor.author Nollmann, Marceloca
dc.date.accessioned 2018-06-25T11:25:30Z
dc.date.available 2018-06-25T11:25:30Z
dc.date.issued 2017
dc.description.abstract At the kilo- to megabase pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combine high-content super-resolution microscopies with state-of-the-art DNA-labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We find that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type. Critically, despite this large heterogeneity, we are able to visualize nanometer-sized epigenetic domains at the single-cell level. In addition, absolute contact frequencies within and between TADs are to a large extent defined by genomic distance, higher-order chromosome architecture, and epigenetic identity. We propose that TADs and compartments are organized by multiple, small-frequency, yet specific interactions that are regulated by epigenetics and transcriptional state.
dc.description.sponsorship This research was supported by funding from the European Research Council under the 7th Framework Program (FP7/2010-2015, ERC grant agreement 260787 to M.N. and FP7/2007-2013, and ERC grant agreement 609989 to M.A.M.-R.). M.A.M.-R. and G.C. acknowledge support from the European Union's Horizon 2020 research and innovation program under grant agreement 676556. This work has also benefited from support by the Labex EpiGenMed, an «Investments for the future» program, reference ANR-10-LABX-12-01, the Spanish Ministry of Economy and Competitiveness (BFU2013-47736-P to M.A.M.-R.), and from “Centro de Excelencia Severo Ochoa 2013-2017”, SEV-2012-0208 to the CRG. 3D-SIM experiments were performed at Montpellier Resource Imaging. We acknowledge the France-BioImaging infrastructure supported by the French National Research Agency (ANR-10-INBS-04, «Investments for the future»).
dc.format.mimetype application/pdf
dc.identifier.citation Cattoni DI, Cardozo Gizzi AM, Georgieva M, Di Stefano M, Valeri A, Chamousset D et al. Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions. Nat Commun. 2017 Nov 24;8(1):1753. DOI: 10.1038/s41467-017-01962-x
dc.identifier.doi http://dx.doi.org/10.1038/s41467-017-01962-x
dc.identifier.issn 2041-1723
dc.identifier.uri http://hdl.handle.net/10230/34963
dc.language.iso eng
dc.publisher Nature Publishing Groupca
dc.relation.ispartof Nature Communications. 2017 Nov 24;8(1):1753
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/260787
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/609989
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676556
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2013-47736-P
dc.rights © The Author(s) 2017. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.keyword Computational biology and bioinformatics
dc.subject.keyword Epigenomics
dc.subject.keyword Nanoscale biophysics
dc.subject.keyword Super-resolution microscopy
dc.title Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactionsca
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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