Coding and potential regulatory sequences of a cluster of chorion genes in Drosophila melanogaster

We have characterized at the nucleotide level a 4.8-kilobase pair segment of the third chromosome of Drosophila melanogaster, which contains a cluster of three chorion genes, s18-1, s15-1 and s19-1. These genes are tandemly oriented and share the same basic organization: a small and a large exon separated by a short intron in the signal peptide region. In the coding region, limited similarities at the DNA and protein level suggest a common but distant evolutionary origin. The flanking sequences were searched for elements that might be involved in controlling the tissue-specific and temporally regulated expression and the selective amplification of the chorion genes. A good candidate for a cis-regulatory element is the hexamer, TCACGT, which is found in all three genes in a highly significant position, 23 to 27 nucleotides upstream of the TATA-box, accompanied by additional, less exact similarities. Palindromes and short inverted repeats that are found in the vicinity of their complement are non-uniformly distributed: they are most concentrated in the 3' flanking part of all three genes, in and near regions of unusually high A and T content. The highest number of dyad symmetries, reminiscent of sequences that function as viral replication origins, is found associated with the T- and A-rich regions between genes s18-1 and s15-1.