Sequence-directed bends of DNA helix axis at the upstream activation sites of α-cell-specific genes in yeast

The MFα1 gene of Saccharomyces cerevisiae, a major structural gene for mating pheromone α factor, is an α-cell-specific gene whose expression is regulated by the mating-type locus, MAT. Two upstream activation sites (UAS_MFα1s), which are binding sites for an activator protein, MATα1 , mediate α-cell-specific expression of this gene. We show here that DNA fragments containing the UAS_MFα1 region exhibited anomalous slow electrophoretic mobilities on gels at lower temperature, but not at higher temperature, that is characteristic of bent DNA. We confirmed the sequence-directed bend at the UAS_MFα1 region by employing a circular permutation analysis and a DNA cyclization assay. Deletion analyses revealed the existence of two bends in this region, each of which overlaps each UAS_MFα1 element. The two bends were almost in phase; they lie in a nearly same plane with a same direction. We also show the existence of sequence-directed bend at the UAS region of the STE3 gene, another α-specific gene in S. cerevisiae. These bent DNAs may be involved in transcriptional regulation of this set of genes.