PMID: 11342213May 9, 2001Paper

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

Biochimica Et Biophysica Acta
G V GlazkoM V Glazkov

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 sequ...Continue Reading

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Citations

Jan 6, 2010·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Juan Carlos Rivera-Mulia, Armando Aranda-Anzaldo
May 31, 2006·Biochemistry. Biokhimii︠a︡·A FioriniM A Fernandez
Mar 6, 2007·BMC Bioinformatics·Kenneth EvansLorenz Wernisch
Aug 23, 2005·Virology Journal·Chassidy N Johnson, Laura S Levy
Oct 3, 2012·PloS One·Galina V GlazkoIgor B Rogozin
Dec 15, 2006·Plant Biotechnology Journal·Apolonia H M Van der GeestWilliam M Ainley
Jul 19, 2006·Cellular & Molecular Biology Letters·Adrian E PlattsStephen A Krawetz
Aug 24, 2002·The Journal of Immunology : Official Journal of the American Association of Immunologists·Peter GoebelAnn J Feeney
Jun 15, 2004·Gene·Zdenek TrachtulecJiri Forejt

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