Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix

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 1 Elsevier Science B.V. All rights reserved.