Mapping and positioning DNA-binding proteins along genomic DNA. Structure ofD.melanogasterribosomal ′Alu-repeats′ and 1.688 satellite chromatin

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Abstract
Chromatin structure of so-called ′Alu-repeat′ in D.melanogaster ribosomal non-transcribed spacer that contains sequences homologous to the promoter of ribosomal genes has been studied. Using the ′protein image′ hybridization assay based on UV-light-induced DNA-protein crosslinking and 2-D gel retardation electrophoresis, two proteins of the molecular mass of 50 kD (rABP50) and 70 kD (rABP70), associated with ′Alu-repeat′ DNA have been found. Exo III mapping of crosslinking sites and DNase I footprinting have provided a detailed map of H1, rABP50 and rABP70 contacts within the ′Alu-repeat′ and H1 and a nonhistone protein contacts on satellite DNA. These data indicate precise positioning of non-histone proteins, histone H1 and nucleosomes within genomic regions studied and account for the presence of unusual 240 bp long nucleosomal particles in ′Alu-repeats′. The same approach can be adapted for succesive mapping and positioning proteins on genomic DNA.