Gv. Glazko et al., Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix, BBA-GENE ST, 1517(3), 2001, pp. 351-364
Citations number
56
Categorie Soggetti
Molecular Biology & Genetics
Journal title
BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION
Scaffold/matrix-associated region (S/MAR) sequences are DNA regions that ar
e attached to the nuclear matrix, and participate in many cellular processe
s. The nuclear matrix is a complex structure consisting of various elements
. In this paper we compared frequencies of simple nucleotide motifs in S/MA
R sequences and in sequences extracted directly from various nuclear matrix
elements, such as nuclear lamina, cores of rosette-like structures, synapt
onemal complex, Multivariate linear discriminant analysis revealed signific
ant differences between these sequences. Based on this result we have devel
oped a program, ChrClass (Win/NT version, ftp.bionet.nsc.ru/pub/biology/chr
class/ chrclass.zip), for the prediction of the regions associated with var
ious elements of the nuclear matrix in a query sequence. Subsequently, seve
ral test samples were analyzed by using two S/MAR prediction programs (a Ch
rClass and MAR-Finder) and a simple MRS criterion (S/MAR recognition signat
ure) indicating the presence of S/MARs. Same overlap between the prediction
s of all MAR prediction tools has been found. Simultaneous use of the ChrCl
ass, MRS criterion and MAR-Finder programs may help to obtain a more clearc
ut picture of S/MAR distribution in a query sequence. In general, our resul
ts suggest that the proportion of missed S/MARs is lower for ChrClass, wher
eas the proportion of wrong S/MARs is lower for MAR-Finder and MRS. (C) 200
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