title: Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix.
abstract: Scaffold/matrix-associated region (S/MAR) sequences are DNA regions that are attached to the nuclear matrix, and participate in many cellular processes. The nuclear matrix is a complex structure consisting of various elements. In this paper we compared frequencies of simple nucleotide motifs in S/MAR sequences and in sequences extracted directly from various nuclear matrix elements, such as nuclear lamina, cores of rosette-like structures, synaptonemal complex. Multivariate linear discriminant analysis revealed significant differences between these sequences. Based on this result we have developed a program, ChrClass (Win/NT version, ftp.bionet.nsc.ru/pub/biology/chrclass/chrclass.zip), for the prediction of the regions associated with various elements of the nuclear matrix in a query sequence. Subsequently, several test samples were analyzed by using two S/MAR prediction programs (a ChrClass and MAR-Finder) and a simple MRS criterion (S/MAR recognition signature) indicating the presence of S/MARs. Some overlap between the predictions of all MAR prediction tools has been found. Simultaneous use of the ChrClass, MRS criterion and MAR-Finder programs may help to obtain a more clearcut picture of S/MAR distribution in a query sequence. In general, our results suggest that the proportion of missed S/MARs is lower for ChrClass, whereas the proportion of wrong S/MARs is lower for MAR-Finder and MRS.
authors.affiliation: Institute of Cytology and Genetics, Novosibirsk, Russia. gvg2@psu.edu
authors.forename: G V
authors.initials: GV
authors.lastname: Glazko
authors.forename: I B
authors.initials: IB
authors.lastname: Rogozin
authors.forename: M V
authors.initials: MV
authors.lastname: Glazkov
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification; D018744:DNA, Plant / Q000235:genetics / Q000302:isolation & purification; D002523:Edible Grain / Q000235:genetics; D005914:Globins / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D015530:Nuclear Matrix / Q000737:chemistry / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods / Q000706:statistics & numerical data; D012984:Software; D016615:Telomere / Q000235:genetics
chemical_list: D018744:DNA, Plant; D005914:Globins; D004247:DNA