Cold Spring Harb Symp Quant Biol 38: 405-16 (1974)[74174452]
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.
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