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. 1990 Oct;10(10):5378–5387. doi: 10.1128/mcb.10.10.5378

Z-DNA formation in the rat growth hormone gene promoter region.

M J Thomas 1, T M Freeland 1, J S Strobl 1
PMCID: PMC361237  PMID: 2398895

Abstract

The complete DNA sequence of the 1.7 kilobase pairs (kbp) 5' of the rat growth hormone gene (rGH) has been determined and analyzed for Z-DNA-forming potential. Regions of alternating purine-pyrimidine (APP) sequences located between -1047 and -986 [(GT)31], between -445 and -433 bp, and between -426 and -403 bp relative to the rGH RNA transcription initiation site were identified and shown to form Z-DNA in negatively supercoiled plasmids by two-dimensional gel electrophoresis. Free-energy calculations indicated that Z-DNA forms most readily in the proximal Z-DNA regions. Diethyl pyrocarbonate footprinting of physiologically supercoiled plasmid DNA confirmed the presence of Z-DNA from -444 to -404 bp spanning the two most proximal APP sequences and a short non-APP sequence in between. DNA sequence analysis also predicted a region of DNA curvature near this proximal Z-DNA region. Formation of Z-DNA in the distal Z-DNA region consisting of a (GT)31 repeat was constrained at physiological plasmid superhelical densities. This may be related to the presence of DNA sequences (-1584 to -1559) 512 bp upstream of (GT)31 that undergo cruciform formation and thereby utilize the available free energy. Removal of 580 bp containing the cruciform region resulted in Z-DNA formation within (GT)31, thus demonstrating that deletion mutations can exert topological changes at a distance within the rGH 5'-flanking region. Methylation of two specific cytosines in the rGH 5'-flanking DNA that have been associated with inhibition of rGH promoter activity had no effect on Z-DNA formation. No evidence for DNA secondary structure formation within the rGH second exon-intron or 3'-flanking region was observed. We conclude that the rGH 5'-flanking region undergoes secondary-structure formation at physiological superhelical densities, thus providing a potential mechanism(s) for modulating rGH activity.

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Selected References

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