Altered gene expression correlates with DNA structure.

Abstract

We examined the participation of triplex DNA structure in gene regulation using a poly(dG)-poly(dC) sequence as a model. We show that a poly(dG)-poly(dC) sequence, which can adopt an intramolecular dG.dG.dC triplex under superhelical strain, strongly augments gene expression when placed 5' to a promoter. The activity of this sequence exhibits a striking length dependency: dG tracts of 27-30 bp augment the expression of a reporter gene to a level comparable to that observed with the polyoma enhancer in mouse LTK-cells, whereas tracts of 35 bp and longer have virtually no effect. A supercoiled plasmid containing a dG tract of 30 bp competes in vivo for a trans-acting factor as revealed by reduction in the reporter gene transcription driven by the (dG)29/promoter of the test plasmid, while dGs of 35 bp and longer in the competition plasmid failed to compete. In purified supercoiled plasmid DNA at a superhelical density of -0.05, dG tracts of 32 bp and longer form a triplex, whereas those of 30 bp and shorter remain double-stranded under a PBS solution. These results suggest that a localized superhelical strain can exist, at least transiently, in mouse LTK-cells, and before being relaxed by topoisomerases this rapidly induces dG tracts of 35 bp and longer to adopt a triplex preventing the factor from binding. Thus, these data suggest that a poly(dG)-poly(dC) sequence can function as a negative regulator by adopting an intramolecular triple helix structure in vivo.

The BCL2 major breakpoint region (mbr) regulates gene expression

“…The BCL2 mbr forms triplex DNA under physiological conditions and this non-B DNA is a critical structure for cleavage within the BCL2 mbr that leads to the t(14;18) translocation (Raghavan et al, 2005). Triplex DNA can modulate gene expression both in vivo and when placed upstream of a reporter gene (Kohwi and Kohwi-Shigematsu, 1991;Grigoriev et al, 1992;Kato and Shimizu, 1992). However, the BCL2 mbr, located within the 3 0 -UTR of the gene, is approximately 200-kb downstream from the promoter.…”

Sticky DNA, a Self-associated Complex Formed at Long GAA·TTC Repeats in Intron 1 of the Frataxin Gene, Inhibits Transcription

“…Two mechanisms have been proposed to explain the transcriptional inhibition by triplexes. Formation of a triplex may block the transcription elongation by RNA polymerase (29 -31) or may interfere with the binding of transacting factors to sequences that control transcription (32)(33)(34). Recently, Grabczyk and Usdin proposed another model, in which an RNA polymerase advancing within a long GAA⅐TTC repeat causes the transient formation of an R⅐R⅐Y type of triplex, which then creates a pause site (35).…”

Molecular characterization of a common fragile site ( FRA7H ) on human chromosome 7 by the cloning of a simian virus 40 integration site

“…Hence, we searched the FRA7H region for two types of potential non-B-DNA sequences under negative superhelical strain: triple helixes and MARs. Triple-helix-forming sequences play an important role in triggering gene expression and homologous recombination (43), block DNA replication in vitro (44), and decrease the efficiency of replication in vivo (45). The MARs are prone to unwinding by continuous base unpairing (46).…”