Cold Spring Harb Symp Quant Biol 38: 405-16 (1974)
Each chromosome of the Drosophila melanogaster genome may contain only one DNA molecule. Molecules of lengths corresponding to the DNA content of entire chromosomes have been detected (Kavenoff and Zimm, 1973). This simplicity of basic molecular organization of chromosomal DNA emphasizes that sequence arrangement within the DNA must underlie complexities evident in cytological and genetic analyses of the chromosomes. A major cytological complexity is the distinction between condensed heterochromatin and less condensed euchromatin in interphase and prophase stages of mitosis and meiosis. Localization of highly repeated and satellite DNA species to the heterochromatin (Rae, 1970; Gall et al., 1971) has provided a correlation between sequence differentiation of DNA at a molecular level and chromatin differentiation at a cytological level. A finer level of organization has been suggested for centromeric heterochromatin by Kram et al. (1972), who concluded that the highly repeated sequences are interspersed with less repeated sequences.
Another level of chromosomal organization is observed in polytene nuclei in which the genetically active euchromatin has a banded appearance. Analysis of this particular form of organization has posed a fundamental question in the problem of genome organization. Combined genetic and cytological observations have led to the conclusion that only one function is associated with each band (Judd et al., 1972; Hochman, 1971; Lifschytz, 1971) despite each band containing enough DNA, on the average, to code for 20-30 proteins (30,000 base pairs). One solution to the problem is that there are 20-30 tandem repeats of a single gene in each band (Thomas, 1970, 1971). Lee and Thomas (1973) have detected tandemly repeated sequences in the genome of D. melanogaster by the formation of circular molecules after exonuclease resection of linear DNA fragments. They have concluded that the repeats of any one sequence are clustered into a restricted region of the chromosome and that these regions occur largely in the euchromatin. This latter point depends, in part, on their observation that DNA fragments from polytene or diploid nuclei form circles at the same frequency, even though euchromatin DNA is greatly amplified relative to heterochromatin DNA in polytene nuclei (Rudkin, 1969). These conclusions are in conflict with renaturation analyses which indicate that 75-85% of nuclear DNA sequences are present in only a single copy per genome (Laird, 1971; Wu et al., 1972).
In our analysis of the organization of the Drosophila melanogaster genome we have concentrated on the isolation and characterization of the highly repeated DNA species. We have isolated four major (and one minor) satellites representing 80% of the highly repeated sequences. They occur in only a small number of long homogeneous blocks located primarily in the heterochromatin. These satellites comprise 18 % of the genome and account for over half the tandemly repeated sequences as determined by circle formation following exonuclease resection.