The characterization of DINE-1, a short, interspersed repetitive element present on chromosome and in the centric heterochromatin of Drosophila melanogaster

The banded portion of chromosome 4 (the "dot" chromosome) in Drosophila mel anogaster displays some properties of beta-heterochromatin, which is normal ly found within the centric domain of the chromosomes. The nature and distr ibution of repetitive elements on chromosome 4 could play a role in the est ablishment of this unusual chromatin configuration. We describe here one su ch element: a short, interspersed repetitive sequence named DINE-1. Determi nation of a consensus sequence for the element reveals that there are two c onserved regions (A and B) separated by a highly variable spacer. The conse rved sequences are similar to 400 bp long but degenerate at both ends, open ing the possibility that a vet-to-be-discovered mother element may be prese nt in the genome. DINE-1 bears few of the properties of the mammalian short interspersed elements (SINEs) to which it bears a superficial resemblance in size. It does not appear to be the product of reverse transcription and lacks any polymerase LII promoter consensus. The elements are not flanked b y target site duplications and their termini lack direct or inverted repeat s, suggesting that they themselves are not transposable. Our analysis of co smid clones from chromosome 4, and elsewhere in the genome, revealed that t he euchromatic locations of DINE-I are almost exclusively confined to chrom osome 4. In situ hybridization of a DINE-I probe to polytene chromosomes co nfirmed the preferential distribution along 4, in addition to its presence in the centric heterochromatin. This unusual genomic distribution of bias t oward chromosome 4 is also seen in the sibling species, D. simulans, whose dot chromosomes exhibit poorly resolved polytene bands and lack crossing ov er during meiosis like those of D. melanogaster. However, the dot chromosom e of D. virilis, which exhibits a well-defined banded structure on polytene chromosomes and can cross over, has only a single, discrete site of DINE-1 element hybridization, The presence of DINE-1 within these regions suggest s a role in the heterochromatic nature of chromosome 4 in D. melanogaster a nd supports the contention that repeats accumulate in regions of diminished crossing pears over.