Differential nuclear scaffold/matrix attachment marks expressed genes

Amelia Linnemann, Adrian E. Platts, Stephen A. Krawetz

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)645-654
Number of pages10
JournalHuman Molecular Genetics
Volume18
Issue number4
DOIs
StatePublished - Feb 4 2009
Externally publishedYes

Fingerprint

Matrix Attachment Regions
Nuclear Matrix
Genes
Genome
Chromosomes, Human, Pair 18
Chromosomes, Human, Pair 14
Comparative Genomic Hybridization
Human Chromosomes
HeLa Cells
Lithium
Gene Expression

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Differential nuclear scaffold/matrix attachment marks expressed genes. / Linnemann, Amelia; Platts, Adrian E.; Krawetz, Stephen A.

In: Human Molecular Genetics, Vol. 18, No. 4, 04.02.2009, p. 645-654.

Research output: Contribution to journalArticle

Linnemann, Amelia ; Platts, Adrian E. ; Krawetz, Stephen A. / Differential nuclear scaffold/matrix attachment marks expressed genes. In: Human Molecular Genetics. 2009 ; Vol. 18, No. 4. pp. 645-654.
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