Transitions in topological organization of supercoiled DNA domains as a potential regulatory mechanism

DNA structure and function

The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase.

DNA conformational variations in the in vitro torsionally strained Ig kappa light chain gene localize on consensus sequences

We have analyzed the localization and the dependence upon superhelical density of the DNA sites which modify their conformation under torsional strain in a mouse Ig L kappa gene. The conformational variations occur on DNA sites which have been defined as protein interaction sites and consensus sequence motifs: the 5'-upstream regulatory decanucleotides, the TATA sequence, the consensus heptanucleotides of the J recombinational sequences.

Sensitivity of intergenic regions of yeast mitochondrial DNA to single-strand-specific nucleases

The reactivity of mitochondrial DNA (mtDNA) sequences from Torulopsis glabrata and Saccharomyces cerevisiae towards single-strand-specific nucleases has been examined. AT-rich stretches located in intergenic sequences from both yeasts were cleaved by nucleases when the sequences were contained in supercoiled plasmid DNA. In particular ori/rep sequences from the mtDNA of S. cerevisiae were shown to be sensitive to the single-strand-specific nucleases. The locations of the sensitive sites were related to the organisation of the sequence domains of ori/rep and the superhelicity of the DNA, as well as the presence of particular sequences. It is proposed that distortions of the DNA duplex could be generated in mtDNA molecules in vivo and that these distortions may provide a substrate for enzymes involved in transmission, recombination and/or transcription of mtDNA.

Purified Saccharomyces cerevisiae RNA polymerase II interacts homologously with two different promoters as revealed by P1 endonuclease analysis

The intergenic region of the Saccharomyces cerevisiae GAL1-GAL10 divergent promoters has been circularized in vitro in different topological states. In defined conditions, purified homologous RNA polymerase II forms two stable complexes (half-life approximately equal to 5 h) with this DNA in the presence of the four ribonucleotides, as determined by measurement (Gamper and Hearst 1983) of the amount and stability of the resulting unwinding. Each stable complex induces in the closed DNA domain a region of hypersensitivity to P1 endonuclease. The two induced hypersensitive regions are very similar: each maps on one promoter, spans over the 100 bp DNA sequence that encompasses the RNA Initiation Sites (RIS) and the TATA box, is composed by three subregions (one on the RIS, one proximal or overlapping the TATA sequence, one intermediate). We show that this promoter-localized interaction is supercoil-dependent.

Persistence of cruciform structure and preferential location of nucleosomes on some regions of pBR322 and ColE 1 DNAs

Inverted repeats of pBR322 and ColE 1 DNAs have been analyzed for the presence of cruciform structures upon formation of nucleosomes, using S1, P1 and restriction enzyme analysis. In both cases the fraction of molecules showing nuclease-sensitive sites is unaffected by the DNA relaxation, owing to the formation of nucleosomes. A kinetic mechanism, based on the freezing of cruciform structures on the nucleosome surface or nearby, is proposed. This hypothesis is supported by a preferential location of nucleosomes at the DNA sequences containing the nuclease-sensitive sites, as indicated by restriction enzyme analysis and electron microscopy visualization after psoralen cross-linking.

Differential modulation by spermidine of reactions catalyzed by type 1 prokaryotic and eukaryotic topoisomerases

In the absence of DNA aggregation, spermidine inhibited the relaxation of negatively supercoiled DNA by Escherichia coli topoisomerase I at concentrations of the polyamine normally found intracellularly. Spermidine also curtailed the cleavage of negatively supercoiled ColE1 DNA by the enzyme in the absence of Mg2+. On the contrary, knotting of M13 single-stranded DNA circles catalyzed by topoisomerase I was stimulated by the polyamine. Relaxation of supercoiled DNA by eukaryotic type 1 topoisomerases, such as calf thymus topoisomerase I and wheat germ topoisomerase, was significantly stimulated by spermidine in the same range of concentrations that inhibited the prokaryotic enzyme. In reactions catalyzed by S1 nuclease, the polyamine enhanced the digestion of single-stranded DNA and inhibited the nicking of negatively supercoiled DNA. These results suggest that spermidine modifies the supercoiled duplex substrate in these reactions by modulating the degree of single strandedness.