Studies of an 800-kilobase DNA stretch of the Drosophila X chromosome: comapping of a subclass of scaffold-attached regions with sequences able to replicate autonomously in Saccharomyces cerevisiae.

Abstract

We have previously mapped scaffold-attached regions (SARs) on an 800-kilobase DNA walk from the Drosophila X chromosome. We have also previously shown that the strength of binding, i.e., the ability of SARs to bind to all nuclear scaffolds or only to a fraction of them varied from one SAR to another one. In the present study, 71 of the 85 subfragments that bind scaffolds and 38 fragments that do not bind scaffolds were tested for their ability to promote autonomous replicating sequence (ARS) activity in Saccharomyces cerevisiae. Sixteen SAR-containing fragments from the chromosome walk were also examined for association to yeast nuclear scaffolds in vitro. All identified ARSs (a total of 27) were present on SAR-containing fragments, except two, which were adjacent to SARs. There is thus a correlation between ARS and SAR activities, and this correlation defines a SAR subclass. Moreover, the presence of an ARS on a DNA fragment appeared to be highly correlated with the strength of binding. The binding activity was highly conserved from Drosophila melanogaster to yeast. These data suggest that Drosophila DNA sequences responsible for binding to components of the nuclear scaffold from either D. melanogaster or yeast may be involved in the process of heterologous extrachromosomal replication in yeasts.Electron microscopic and sedimentation analyses of histone-depleted chromosomes and nuclei (5, 14, 40, 52) support the hypothesis that eucaryotic DNA is organized as individual loops constrained at their bases by interaction of DNA with nonhistone proteins. Laemmli and co-workers (37) have proposed an extraction procedure in which lithium 3'-5'-diiodosalicylate (LIS) is used to isolate specific DNA fragments which presumably form the bases of the loops. This technique has been applied to various parts of the

Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants,

“…These putative structural elements of chromatin have attracted considerable attention because of evidence for their involvement in the regulation of transcription, including stabilization and increased levels of transgene expression (12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) [reviewed by Bode et al (4)]. The comapping of MARs and origins of replication and the functioning of MARs as ARS elements suggest a role for MARs in DNA replication (28)(29)(30)(31)(32)(33)(34).…”

Matrix attachment regions and structural colinearity in the genomes of two grass species

“…These two neighboring attachment sites delineate a putative loop of ∼6.6 kb containing the Sh2 homolog. It should be pointed out that different functions have been suggested for strong and weak MARs (2,15) and that, in at least one case, involvement of a strong MAR in attenuating transgene silencing has been reported (9). While this is certainly an interesting issue, it is beyond the scope of this work.…”

“…Hence, most of the existing information on the structural organization of the genome describes individual genes and their immediate surroundings. Information on domain organization and chromosome folding at a supragenic level in animal systems is limited to only a few studies: a 320 kb continuum of the Drosophila rosy-Ace locus (13), an 800 kb region of Drosophila chromosome 1 (14,15), the 240 kb amplicon of the chinese hamster dihydrofolate reductase gene (16) and 200 kb around the mouse heavy chain IgH locus (17). The first study in plants devoted to the higher order structural organization of a large chromosomal continuum was focused on a 290 kb region around maize Adh1 (18).…”

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

“…S/MARs anchor chromatin onto the NM, thereby organizing the genomic DNA into topologically distinct loop domains that are important for the regulation of replication and transcription. 2 Despite numerous genomic studies, [3][4][5][6][7] no consensus S/MAR sequence has been identified so far. 8 S/MARs can be both A/T 9 or G/C rich.…”