Arrangement of the highly reiterated DNA sequences in the centric heterochromatin of Drosophila melanogaster. Evidence for interspersed spacer DNA.

We have investigated the arrangement of the highly reiterated centromeric DNA sequences in Drosophila melanogaster by studying the physical properties of sequences obtained after the hydroxyapatite isolation of rapidly renaturing molecules. It was found that the fraction of material recovered as partially renatured varied with the molecular weight of the starting material, although conservative length corrections on the chosen Cot values were made. On banding in a CsCl gradient a bimodal distribution for the renatured molecules was found. This bimodal distribution was also sensitive to the molecular weight of the single strand material. The peaks were shown to consist of respectively: h.a.r.r.DNAt sequences and renatured h.a.r.r.DNA sequences with attached unrenatured “spacer” sequences. From melting curve data, RNA-DNA hybridization and kinetic analysis other explanations for the increased yield and bimodal distribution of the renatured molecules could be ruled out. Computer simulation of a random shear process on a DNA sequence which alternates an h.a.r.r.DNA sequence from one to three times larger than the spacer sequence can be seen to fit the experimental situation. We conclude that the constitutive heterochromatin is composed of blocks of extremely simple sequences stretching from 1.5 to 6 million daltons interspersed by a more complex sequence of molecular weights of approximately 2 to 4 million daltons. A similar interspersion of sequences for the mouse satellite DNA was found, though preliminary data suggest that the stretches of mouse satellite may be much longer. The occurrence of a more complex DNA at this locus of the Drosophila chromosome raises some interesting possibilities for both the genetic potential of this area and for chromosomal “housekeeping” functions.