title: A bipartite sequence element associated with matrix/scaffold attachment regions.
abstract: 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.
authors.affiliation: E. C. Slater Instituut, BioCentrum Amsterdam, University of Amsterdam, Plantage Muidergracht 12, 1018 TV Amsterdam, The Netherlands.
authors.forename: C M
authors.initials: CM
authors.lastname: van Drunen
authors.forename: R G
authors.initials: RG
authors.lastname: Sewalt
authors.forename: R W
authors.initials: RW
authors.lastname: Oosterling
authors.forename: P J
authors.initials: PJ
authors.lastname: Weisbeek
authors.forename: S C
authors.initials: SC
authors.lastname: Smeekens
authors.forename: R
authors.initials: R
authors.lastname: van Driel
mesh_terms: D000818:Animals; D034961:Antigens, Nuclear; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence / Q000235:genetics; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005057:Eukaryotic Cells / Q000166:cytology / Q000378:metabolism; D016678:Genome; D005914:Globins / Q000235:genetics; D006801:Humans; D019901:Locus Control Region / Q000235:genetics; D015530:Nuclear Matrix / Q000378:metabolism*; D009687:Nuclear Proteins / Q000378:metabolism*; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*
chemical_list: D034961:Antigens, Nuclear; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D009707:Nucleosomes; D005914:Globins; D004247:DNA