Differential nuclear scaffold/matrix attachment marks expressed genes.
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.
Linnemann
Amelia K
AK
The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, C.S. Mott Center, Detroit, MI48201, USA.
Platts
Adrian E
AE
Krawetz
Stephen A
SA
D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006367:HeLa Cells; D006801:Humans; D045170:Matrix Attachment Regions; D015530:Nuclear Matrix / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding