Scaffold-associated regions and repeated or cross-hybridizing sequences on an 800 kilobase DNA stretch of the Drosophila X chromosome.

DNA fragments binding to the scaffold (SARs) have been previously mapped on an 800-kb DNA fragment from the Drosophila X chromosome. Here we have examined whether these 86 DNA fragments bear sequences repeated in the Drosophila genome and/or cross-hybridizing sequences. Twenty-two middle-repeated sequences were localized by hybridizing Southern transfers of representative cloned DNA with total genomic DNA and, reciprocally, by hybridizing Southern transfers of total genomic DNA with this cloned DNA. Seventy-nine out of the 86 SAR-containing fragments appeared to be distinct from these 22 repeated motifs. Therefore, SARs, in their vast majority, are not members of middle-repeated sequence families. However, the 22 middle-repeated sequences were shown to be significantly located in the near vicinity of SARs. Hybridizations were also performed between SAR-containing DNA fragments, either at a high or at a low stringency. At a high stringency, the 86 SAR-containing DNA fragments did not cross-hybridize. However, at a low stringency, a complex hybridization network was evidenced. These nucleotide sequence similitudes support the idea that the various SARs may play common roles.