Nucleic Acids Research, 2000, Vol. 28, No. 21 4083-4089
© 2000 Oxford University Press
Poly(dA·dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo
Institut für Zellbiologie, ETH-Zürich, Hönggerberg, CH-8093 Zürich, Switzerland
Poly(dA·dT) sequences (T-tracts) are abundant genomic DNA elements with unusual properties in vitro and an established role in transcriptional regulation of yeast genes. In vitro T-tracts are rigid, contribute to DNA bending, affect assembly in nucleosomes and generate a characteristic pattern of CPDs (cyclobutane pyrimidine dimers) upon irradiation with UV light (UV photofootprint). In eukaryotic cells, where DNA is packaged in chromatin, the DNA structure of T-tracts is unknown. Here we have used in vivo UV photofootprinting and DNA repair by photolyase to investigate the structure and accessibility of T-tracts in yeast promoters (HIS3, URA3 and ILV1). The same characteristic photofootprints were obtained in yeast and in naked DNA, demonstrating that the unusual T-tract structure exists in living cells. Rapid repair of CPDs in the T-tracts demonstrates that these T-tracts were not folded in nucleosomes. Moreover, neither datin, a T-tract binding protein, nor Gcn5p, a histone acetyltransferase involved in nucleosome remodelling, showed an influence on the structure and accessibility of T-tracts. The data support a contribution of this unusual DNA structure to transcriptional regulation.
* To whom correspondence should be addressed. Tel: +41 1 633 33 23; Fax: +41 1 633 10 69; Email: thoma@cell.biol.ethz.ch Present address: Bernhard Suter, Department of Molecular and Cell Biology, 222 Stanley Hall, Berkeley, CA 9472, USA
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