A bipartite sequence element associated with matrix/scaffold attachment regions.

@article{citeulike:435742, 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.}, address = {E. C. Slater Instituut, BioCentrum Amsterdam, University of Amsterdam, Plantage Muidergracht 12, 1018 TV Amsterdam, The Netherlands.}, author = {van Drunen, C. M. and Sewalt, R. G. and Oosterling, R. W. and Weisbeek, P. J. and Smeekens, S. C. and van Driel, R. }, citeulike-article-id = {435742}, issn = {0305-1048}, journal = {Nucleic Acids Res}, keywords = {mar, smar}, month = {July}, number = {14}, pages = {2924--2930}, posted-at = {2005-12-12 12:10:15}, priority = {0}, title = {A bipartite sequence element associated with matrix/scaffold attachment regions.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/10390535}, volume = {27}, year = {1999} }

TY - JOUR ID - citeulike:435742 L3 - citeulike-article-id:435742 TI - A bipartite sequence element associated with matrix/scaffold attachment regions. JF - Nucleic Acids Res VL - 27 IS - 14 SP - 2924 EP - 2930 AD - E. C. Slater Instituut, BioCentrum Amsterdam, University of Amsterdam, Plantage Muidergracht 12, 1018 TV Amsterdam, The Netherlands. SN - 0305-1048 N2 - 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. KW - mar KW - smar AU - van Drunen, CM AU - Sewalt, RG AU - Oosterling, RW AU - Weisbeek, PJ AU - Smeekens, SC AU - van Driel, R PY - 1999/07/15/ UR - http://view.ncbi.nlm.nih.gov/pubmed/10390535 ER -