Applicability of superhelical model for regulation of gene expression

The superhelical model for regulation of gene expression was tested in 41 structural genes of eukaryotes, viruses and plasmids, and in the primer RNA gene for DNA replication in five kinds of enteric bacteria and two kinds of plasmids. The model which was first proposed for regulation of transcription in simian virus 40 was based on the following observations: a stem-loop structure of low free energy was located 3' downstream from the transcriptional initiation site; sequences homologous to the loop were located at the symmetrical site with the stem-loop at the center; and the loop encountered any of these homologous sequences after one rotation of superhelix depending on the superhelical density. If the loop interacted with the complementary sequences in the opposite strand, DNA formed a specific cruciform or T-shaped structure. The superhelical model proposed that transcription was regulated by the conversion of the template DNA in the regular, the cruciform, and the T-shaped structures. The model was applicable to all the structural genes and the primer RNA genes tested so far, except histone genes. In eukaryotes, only one stem-loop structure which conformed to the superhelical model was constructed in most of the genes except the growth hormone genes, the globin genes of human, and the human interferon gamma gene. An average length of the stem-loop was 46 bases, and the 5' end of the stem loop was located at the 30th base downstream from the transcriptional initiation site on the average in eukaryotes. In some genes, a consensus sequence was detected in the loops of the same kind of gene in different species or of different kind of gene in the same species.