A bipartite sequence element associated with matrix/scaffold attachment regions

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 compos ed of two degenerate sequences (AATAAYAA and AWWRTAANNWWGNNNC) within close proximity, Analysis of >300 kb of genomic sequence from a variety of eukar yotic 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 spec ifically to the nuclear scaffold, Although all MRSs are associated with a S AR, 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 th e nucleosome near the dyad axis, together creating a putative protein bindi ng site. The identification of a MAR- and SAR-associated DNA element is an important step forward towards understanding the molecular mechanisms of th ese 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 an d analysis of proteins that specifically bind to the MRS.