An effect of DNA sequence on nucleosome occupancy and

A barrier phases nucleosomes at the yeast (S. cerevisiae) GAL1/10 genes. Here we separate nucleosome positioning from occupancy, and show that the degree of occupancy of these phased sites is predictably determined by the underlying DNA sequences. As this occupancy is increased (by sequence alteration) nucleosome removal upon induction is decreased, as is mRNA production. These results explain why promoter sequences have evolved to form nucleosomes relatively inefficiently. The UASg, the yeast regulatory locus that bears binding sites for the activator Gal4, also bears binding sites for the protein RSC1. A RSC/partially-unwound nucleosome complex constitutively covers the UASg and presents Gal4 binding sites for ready access by the activator. By virtue of its tight positioning, the complex also comprises a barrier to what would otherwise be encroaching nucleosomes and, as a result, nucleosomes flanking the UASg are unusually tightly positioned, or phased. This positioning is effected in different sequence contexts1. Here we contrast nucleosome positioning (i.e. the location of the phased sites adjacent to the UASg, essentially the same in every member of the population), wit