Book of Abstracts: Albany 2007
June 19-23 2007
MARs Incorporate Strong Nucleosome-positioning Sites with TopoII Binding in the Vicinity
Matrix attachment regions (MARs) can be defined as DNA fragments that bind to the nuclear matrix. They form by these means the anchorage points of torsionally constrained loop domains of DNA. Nucleotide sequence of MARs has some context characteristics: polyA, polyT, different TG motives, purine-pyrimidine sequences, ?kinked? DNA signals. For sequences of MARs it seems that the localization of these characteristics are not put in order. For the sequences published in literature previously, we constructed the maps of nucleosome-positioning sites obtained by the combined method that we proposed earlier. These maps incorporate Topoisomerase II sites also as well as some context characteristics. For the analysis we have used 18 nucleotide sequences of MARs of region length from ∼300 bp up to ∼11 kbp. As it is shown short MARs of ∼300 bp (Homo sapiens) may not incorporate even medium nucleotide-positioning sites, but include TopoII sites (consensus of recognition for vertebrates). Especially strong nucleosome-positioning sites are presented in the sequence of MARs beginning with ∼800 bp (95% of the analyzed sequences longer then 800 bp). With the length increasing they may incorporate two or more strong nucleosome-positioning sites along with medium ones that may imply multiple or alternative variants of anchorage. The majority of strong nucleotide-positioning sites are contiguous of minimal potential of nucleosome-positioning. These fragments of minimal potential incorporate TopoII sites. For some sequences they are experi-mentally determined earlier and for others are predicted by TopoII consensus for verterbrates. Strong nucleosome-positioning sites may incorporate small An,Tn tracts (n=3,4,5). Long mononucleotide tracts are not incorporated in them. There is no significant correlation of other types of context characteristics with the strong nucleosome-positioning sites.
Fedoseyeva V. B.*
Institute of Molecular Genetics