A bipartite sequence element associated with matrix/ scaffold attachment regions

• Published in: Nucleic acids research Vol. 27; no. 14; pp. 2924 - 2930
• Main Authors: van Drunen, Cornells M., Sewalt, Richard G. A. B., Oosterling, Rob W., Weisbeek, Peter J., Smeekens, Sjef C. M., van Driel, Roel
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.07.1999; Oxford Publishing Limited (England)
• Subjects: Animals; Antigens, Nuclear; Arabidopsis - genetics; Base Sequence; Binding Sites; Caenorhabditis elegans - genetics; Cell Nucleus - genetics; Cell Nucleus - metabolism; Conserved Sequence - genetics; DNA - genetics; DNA - metabolism; DNA-Binding Proteins - metabolism; Eukaryotic Cells - cytology; Eukaryotic Cells - metabolism; Genome; Globins - genetics; Humans; Locus Control Region - genetics; Nuclear Matrix - metabolism; Nuclear Proteins - metabolism; Nucleosomes - genetics; Nucleosomes - metabolism; Regulatory Sequences, Nucleic Acid - genetics
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/27.14.2924

We have identified a MAR/SAR recognition signature (MRS) which is common to a large group of matrix and scaffold attachment regions. The MRS is composed of two degenerate sequences (AATAAYAA and AWWRTAANNWWGNNNC) within close proximity. Analysis of <300 kb of genomic sequence from a variety of eukaryotic organisms shows that the MRS faithfully predicts 80% of MARs and SARs. In each case where we find a MRS, the corresponding DNA region binds specifically to the nuclear scaffold. Although all MRSs are associated with a SAR, not all known SARs and MARs contain a MRS, suggesting that at least two classes exist, one containing a MRS, the other not. Evidence is presented that the two sequence elements of the bipartite MRS occupy a position on the nucleosome near the dyad axis, together creating a putative protein binding site. The identification of a MAR- and SAR-associated DNA element is an important step forward towards understanding the molecular mechanisms of these elements. It will allow: (i) analysis of the genomic location of SARs, e.g. in relationship to genes, based on sequence information alone, rather than on the basis of an elaborate biochemical assay; (ii) identification and analysis of proteins that specifically bind to the MRS.