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dc.contributor.authorDobson, Jason
dc.contributor.authorHong, Deli
dc.contributor.authorBarutcu, Rasim
dc.contributor.authorWu, Hai
dc.contributor.authorImbalzano, Anthony N.
dc.contributor.authorLian, Jane B.
dc.contributor.authorStein, Janet L.
dc.contributor.authorVan Wijnen, Andre J.
dc.contributor.authorNickerson, Jeffrey A.
dc.contributor.authorStein, Gary S.
dc.date2022-08-11T08:08:19.000
dc.date.accessioned2022-08-23T15:51:05Z
dc.date.available2022-08-23T15:51:05Z
dc.date.issued2016-09-14
dc.date.submitted2016-12-06
dc.identifier.citationJ Cell Physiol. 2016 Sep 14. doi: 10.1002/jcp.25596. <a href="http://dx.doi.org/10.1002/jcp.25596">Link to article on publisher's site</a>
dc.identifier.issn0021-9541 (Linking)
dc.identifier.doi10.1002/jcp.25596
dc.identifier.pmid27627025
dc.identifier.urihttp://hdl.handle.net/20.500.14038/28812
dc.description.abstractExperimental approaches to define the relationship between gene expression and nuclear matrix attachment regions (MARs) have given contrasting and method-specific results. We have developed a next generation sequencing strategy to identify MARs across the human genome (MAR-Seq). The method is based on crosslinking chromatin to its nuclear matrix attachment sites to minimize changes during biochemical processing. We used this method to compare nuclear matrix organization in MCF-10A mammary epithelial-like cells and MDA-MB-231 breast cancer cells and evaluated the results in the context of global gene expression (array analysis) and positional enrichment of gene-regulatory histone modifications (ChIP-Seq). In the normal-like cells, nuclear matrix-attached DNA was enriched in expressed genes, while in the breast cancer cells, it was enriched in non-expressed genes. In both cell lines, the chromatin modifications that mark transcriptional activation or repression were appropriately associated with gene expression. Using this new MAR-Seq approach, we provide the first genome-wide characterization of nuclear matrix attachment in mammalian cells and reveal that the nuclear matrix-associated genome is highly cell-context dependent.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=27627025&dopt=Abstract">Link to Article in PubMed</a>
dc.relation.urlhttp://dx.doi.org/10.1002/jcp.25596
dc.subjectCell Biology
dc.subjectCellular and Molecular Physiology
dc.subjectComputational Biology
dc.subjectGenomics
dc.subjectMolecular Genetics
dc.titleIdentifying Nuclear Matrix-Attached DNA Across the Genome
dc.typeJournal Article
dc.source.journaltitleJournal of cellular physiology
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/faculty_pubs/1051
dc.identifier.contextkey9445270
html.description.abstract<p>Experimental approaches to define the relationship between gene expression and nuclear matrix attachment regions (MARs) have given contrasting and method-specific results. We have developed a next generation sequencing strategy to identify MARs across the human genome (MAR-Seq). The method is based on crosslinking chromatin to its nuclear matrix attachment sites to minimize changes during biochemical processing. We used this method to compare nuclear matrix organization in MCF-10A mammary epithelial-like cells and MDA-MB-231 breast cancer cells and evaluated the results in the context of global gene expression (array analysis) and positional enrichment of gene-regulatory histone modifications (ChIP-Seq). In the normal-like cells, nuclear matrix-attached DNA was enriched in expressed genes, while in the breast cancer cells, it was enriched in non-expressed genes. In both cell lines, the chromatin modifications that mark transcriptional activation or repression were appropriately associated with gene expression. Using this new MAR-Seq approach, we provide the first genome-wide characterization of nuclear matrix attachment in mammalian cells and reveal that the nuclear matrix-associated genome is highly cell-context dependent.</p>
dc.identifier.submissionpathfaculty_pubs/1051
dc.contributor.departmentUMass Metabolic Network
dc.contributor.departmentDepartment of Cell and Developmental Biology


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