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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Nuclear scaffold and matrix attachment of HeLa chromatin

ABSTRACT: The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively. We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in HeLa cells. LIS or 2 M NaCl solutions followed by restriction digestion with EcoR1 facilitates the separation from scaffold/matrix bound DNA from non bound DNA. Genomic CGH arrays were used to map the relative differences between attached (scaffold/matrix) and non-attached (loop) portions of HeLa DNA. The expression profile of the HeLa cells used for aCGH analysis was also determined.

ORGANISM(S): Homo sapiens

SUBMITTER: Stephen Krawetz

PROVIDER: E-GEOD-13774 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Differential nuclear scaffold/matrix attachment marks expressed genes.

Linnemann Amelia K AK Platts Adrian E AE Krawetz Stephen A SA

Human molecular genetics 20081118 4

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 loc ...[more]

PMID: 19017725

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