GENOMIC TARGETS OF THE SERENDIPITY BETA-ZINC AND DELTA-ZINC FINGER PROTEINS AND THEIR RESPECTIVE DNA RECOGNITION SITES

The closely related Drosophila serendipity (sry) beta (beta) and delta (delta) Cys2-His2 zinc ringer proteins show partly overlapping in vitro DNA binding specificities and distinct patterns of binding sites on polytene chromosomes. Using a newly developed procedure, we identified genomic DNA targets for these two proteins. Both the sry-beta and delta-proteins protect an 18-22 base region from DNase I digestion within each analysed genomic binding site, that includes a 13 bp consensus sequence. The consensus recognition sites sry-beta-5'-YCAGAGATGCGCA-3' and sry-delta-5'-YTAGAGATGGRAA-3' thus differ by nucleotides at four out of 13 positions. They are determinant for specific binding of the sry-beta and delta-proteins, respectively, produced in Escherichia coli or present in Drosophila embryos. We further show that sry-beta is the major (if not exclusive) Drosophila nuclear protein that specifically binds the 5'-CAGAGTGCGC-3' sequence. The identified sry-beta-genomic targets are all contained within single-copy DNA in euchromatic regions of the genome. Two out of the five characterized in detail map at cytological positions coincident with binding sites of the native sry-beta-protein on polytene chromosomes.