Constancy of somatic DNA organization in developmentally regulated regions of the Drosophila genome.

The purpose of this study was to test for the occurrence of changes in the organization, modification, or selective amplification of six developmentally regulated regions of genomic DNA during Drosophila development. Five of the regions contain structural genes, each of which maps at a single chromosomal site; the sixth region contains a dispersed segment that maps at about 30 different sites and appears to be transposable. The RNA transcripts and encoded proteins of the structural genes are major components of the fat body tissue in late third-instar larvae, in contrast to other larval tissues and young embryos in which the transcripts and proteins are hardly detectable. The dispersed segment shows the reverse developmental regulation: the amount of transcript is relatively high in young embryos and low in larval fat bodies. The test for changes in genomic DNA associated with the regulated expression of the six regions was based on comparative restriction mapping of the DNA from these sources. Genomic clones containing the transcribed and also flanking regions of DNA were used as probes to determine the positions of the complementary restriction fragments after electrophoresis in agarose gels. Each test, which involved digesting the genomic DNA samples with one of the endonucleases and probing with one of the clones, produced identical restriction maps for the different samples. The tests are capable of detecting changes in the organization of the cloned regions resulting from addition or removal either of endonuclease cleavage sites or of segments of DNA located between cleavage sites. Because the activities of several of the endonucleases, and probably all, are sensitive to methylation of one of the bases in the DNA recognition sequence, certain modifications of the cloned regions by methylation could also be detected. Although it is not certain that genomic reorganization or modification would have been detected by these tests, the number of endonucleases used was sufficient to provide persuasive evidence that such changes did not occur. Furthermore, the quantitative as well as qualitative similarities of the restriction maps in each test indicated that there was no significant selective amplification of the DNA within the cloned regions.