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Nucleic Acids Research, 1993, Vol. 21, No. 20 4796-4802
© 1993

MOLECULAR BIOLOGY

Mapping and positioning DNA-binding proteins along genomic DNA. Structure of D.melanogaster ribosomal 'Alu-repeats' and 1.688 satellite chromatin

Sergei V. Belikov+, Alexander I. Belgovsky, Marina P. Partolina, Vadim L. Karpov and Andrei D. Mirzabekov*

W.A.Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow 117984,Russia

*To whom correspondence should be addressed.

Received June 24, 1993. Revised September 9, 1993. Accepted September 9, 1993.

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.

+Present address: Karolinska Institutes Department of Cell and Molecular Biology, Medical Nobel Institute, S-17177, Stockholm, Sweden


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