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dc.contributor.authorQuinodoz, Sofia A.
dc.contributor.authorTabak, Barbara
dc.contributor.authorMcDonel, Patrick
dc.contributor.authorGarber, Manuel
dc.contributor.authorGuttman, Mitchell
dc.date2022-08-11T08:08:36.000
dc.date.accessioned2022-08-23T16:01:04Z
dc.date.available2022-08-23T16:01:04Z
dc.date.issued2018-06-04
dc.date.submitted2018-07-18
dc.identifier.citation<p>Cell. 2018 Jun 4. pii: S0092-8674(18)30636-6. doi: 10.1016/j.cell.2018.05.024. <a href="https://doi.org/10.1016/j.cell.2018.05.024">Link to article on publisher's site</a></p>
dc.identifier.issn0092-8674 (Linking)
dc.identifier.doi10.1016/j.cell.2018.05.024
dc.identifier.pmid29887377
dc.identifier.urihttp://hdl.handle.net/20.500.14038/31034
dc.description<p>Full author list omitted for brevity. For the full list of authors, see article.</p>
dc.description.abstractEukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=29887377&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttps://doi.org/10.1016/j.cell.2018.05.024
dc.subjectNuclear structure
dc.subjectRNA DNA interactions
dc.subjectSPRITE
dc.subjectgenome structure
dc.subjecthigher-order nuclear structure
dc.subjectmulti-way interactions
dc.subjectnuclear organization
dc.subjectnuclear speckle
dc.subjectnucleolus
dc.subjectBioinformatics
dc.subjectCell Biology
dc.subjectComputational Biology
dc.subjectGenetic Phenomena
dc.subjectGenomics
dc.subjectMolecular Biology
dc.subjectStructural Biology
dc.titleHigher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
dc.typeJournal Article
dc.source.journaltitleCell
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/garber_lab_pubs/2
dc.identifier.contextkey12504412
html.description.abstract<p>Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.</p>
dc.identifier.submissionpathgarber_lab_pubs/2
dc.contributor.departmentGarber Lab
dc.contributor.departmentProgram in Molecular Medicine
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology


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