Poly(dA center dot dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo

Poly(dA.dT) sequences (T-tracts) are abundant genomic DNA elements with unu sual properties in vitro and an established role in transcriptional regulat ion of yeast genes. In vitro T-tracts are rigid, contribute to DNA bending, affect assembly in nucleosomes and generate a characteristic pattern of CP Ds (cyclobutane pyrimidine dimers) upon irradiation with UV light (UV photo footprint). in eukaryotic cells, where DNA is packaged in chromatin, the DN A structure of T-tracts is unknown. Here we have used in vivo UV photofootp rinting and DNA repair by photolyase to investigate the structure and acces sibility of T-tracts in yeast promoters (HIS3, URA3 and ILV1). The same cha racteristic photofootprints were obtained in yeast and in naked DNA, demons trating that the unusual T-tract structure exists in living cells. Rapid re pair of CPDs in the T-tracts demonstrates that these T-tracts were not fold ed in nucleosomes, Moreover, neither datin, a T-tract binding protein, nor Gcn5p, a histone acetyltransferase involved in nucleosome remodelling, show ed an influence on the structure and accessibility of T-tracts. The data su pport a contribution of this unusual DNA structure to transcriptional regul ation.