Authors
Dobson, JasonHong, Deli
Barutcu, Rasim
Wu, Hai
Imbalzano, Anthony N.
Lian, Jane B.
Stein, Janet L.
Van Wijnen, Andre J.
Nickerson, Jeffrey A.
Stein, Gary S.
Document Type
Journal ArticlePublication Date
2016-09-14Keywords
Cell BiologyCellular and Molecular Physiology
Computational Biology
Genomics
Molecular Genetics
Metadata
Show full item recordAbstract
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.Source
J Cell Physiol. 2016 Sep 14. doi: 10.1002/jcp.25596. Link to article on publisher's siteDOI
10.1002/jcp.25596Permanent Link to this Item
http://hdl.handle.net/20.500.14038/28812PubMed ID
27627025Related Resources
Link to Article in PubMedae974a485f413a2113503eed53cd6c53
10.1002/jcp.25596