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Human Molecular Genetics Advance Access originally published online on November 18, 2008
Human Molecular Genetics 2009 18(4):645-654; doi:10.1093/hmg/ddn394
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Differential nuclear scaffold/matrix attachment marks expressed genes{dagger}

Amelia K. Linnemann1, Adrian E. Platts1,2 and Stephen A. Krawetz1,2,3,*

1 The Center for Molecular Medicine and Genetics 2 Department of Obstetrics and Gynecology 3 Institute for Scientific Computing, Wayne State University School of Medicine, C.S. Mott Center, 275 E Hancock, Detroit, MI 48201, USA

* To whom correspondence should be addressed. Tel: +1 3135776770; Fax: +1 3135778554; Email: steve{at}compbio.med.wayne.edu

Received October 3, 2008; Revised November 1, 2008; Accepted November 17, 2008

It is well established that nuclear architecture plays a key role in poising regions of the genome for transcription. This may be achieved using scaffold/matrix attachment regions (S/MARs) that establish loop domains. However, the relationship between changes in the physical structure of the genome as mediated by attachment to the nuclear scaffold/matrix and gene expression is not clearly understood. To define the role of S/MARs in organizing our genome and to resolve the often contradictory loci-specific studies, we have surveyed the S/MARs in HeLa S3 cells on human chromosomes 14–18 by array comparative genomic hybridization. Comparison of LIS (lithium 3,5-diiodosalicylate) extraction to identify SARs and 2 M NaCl extraction to identify MARs revealed that approximately one-half of the sites were in common. The results presented in this study suggest that SARs 5' of a gene are associated with transcript presence whereas MARs contained within a gene are associated with silenced genes. The varied functions of the S/MARs as revealed by the different extraction methods highlights their unique functional contribution.

{dagger} The array data reported in the publication is available at GEO as GSM346693, GSM346696, GSM346699 and GSM346701.


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