Analysis of the chicken DNA fragments that contain structural sites of attachment to the nuclear matrix: DNA-matrix interactions and replication

Abstract

Ten short DNA fragments have been selected from a library of the nuclear matrix-attached DNA (nmDNA) from chicken erythrocytes by their ability to hybridize with the fraction of chicken replication origins isolated by nascent DNA strand extrusion. The primary structure of these fragments has been determined. Five of the sequences contained a topoisomerase II recognition site. Most of the studied DNA fragments also have a common eight-nucleotide motif, GCAGACCG/A. A sequence-specific DNA-binding protein with a MW of 55 kDa that interacted with this motif has been identified. Some of the cloned DNA fragments promoted an increased level of transient plasmid replication in transfected chicken cells. The ability of plasmid bearing nmDNA fragments to replicate correlated directly with their ability to target plasmids to the nuclear matrix compartment.

In-silico prediction and observations of nuclear matrix attachment

“…Depending on context AATATATTT could serve as an AT rich origin of replication. Accordingly, early replicating sequences have been associated with nuclear matrix binding by nascent strand excision [67,68]. Applying or removing stress always changes the form of superhelical coiling in a manner that is partitioned between its two orthogonal curvature elements, the writhe Wr (number of superhelical turns) and the twist Tw (number of helical turns).…”

DNA polymorphism and epigenetic marks modulate the affinity of a scaffold/matrix attachment region to the nuclear matrix

“…8 S/MARs can be both A/T 9 or G/C rich. 10 Moreover, the strength and specificity of S/MAR attachment to the NM varies during ontogenesis, 11 in cancer 12 and various genetic diseases such as facioscapulohumeral dystrophy (FSHD). 13,14 Several factors potentially affect the association of DNA with the NM.…”

MARs Wars: heterogeneity and clustering of DNA-binding domains in the nuclear matrix

“…Earlier we have cloned several chicken DNA fragments attached to the nuclear matrix in the nuclei of chicken erythrocytes. One of these MARs designated as CO326 was shown to interact with a sequencespecific DNA-binding protein F326 which recognised a motif TCACTGCAGACCGCTTCG [16,17].…”

“…Plasmids and oligonucleotides. The CO326 fragment was excised from the CO326-pTZ construct [17] by BamHI digestion. Double-stranded oligonucleotides 5'-GATCCTCACTGCAGACCGCTTCG-3' (F326) and 5'-TATTTGATAGCAATATTTAGTATTT-3' (control) were ordered from Operon (Germany) as complementary single-stranded oligonucleotides and then annealed according to the manufacturer's protocol.…”