Nucleotide sequence of the initiation site for ribosomal RNA transcription in Drosophila melanogaster: comparison of genes with and without insertions.

The sequence of 470 nucleotides surrounding the initiation site for rRNA transcription in Drosophila melanogaster has been determined. The precise initiation site was determined first by measuring the DNA fragment protected by the rRNA precursor against digestion by the single-strand specific nuclease S1 and second by direct sequence determination of the first 13 nucleotides of the rRNA precursor. Because greater than 80% od rRNA precursor molecules have been shown previously to bear pppA or ppA 5' termini, we assume that they represent the primary transcription product. Short sequence homologies exist with the initiation regions for rRNA transcription of Xenopus laevis and Saccharomyces cerevisiae. We have determined the nucleotide sequence of the initiation region in four cloned ribosomal genes from D. melanogaster which are not interrupted and in four cloned ribosomal genes in which the 28S rRNA coding region is interrupted by a 5-kilobase type 1 insertion. Three uninterrupted genes and three interrupted genes have identical sequences in the entire analyzed region. The remaining two genes have a single identical base substitution at position -17. We have shown previously that interrupted ribosomal genes in D. melanogaster are not effectively transcribed. Because the nucleotide sequences of the region where transcription initiates are identical in genes with or without insertions, we postulate that the presence of the insertion itself may be responsible for the inactivity of the interrupted genes.