J Mol Biol 135: 465-81 (1979)[80140503]
We have determined the complete nucleotide sequence of the monomer
repeating unit of the 1.688 g/cc satellite DNA from Drosophila
melanogaster This satellite DNA, which makes up 4% of the Drosophila
genome and is located primarily on the sex chromosomes, has a repeat
unit 359 base-pairs in length. This complex sequence is unrelated ~
the other three major satellite DNAs present in this species each of
which contains a very short repeated sequence only 5 to 10 base-pairs
long. The repeated sequence is more similar to the complex repeating
units found in satellites of mammalian origin in that it contains
runs of adenylate and thymidylate residues. We have determined the
nature of the sequence variations in this DNA by restriction nuclease
cleavage and by direct sequence determination of (1) individual
monomer units cloned in hybrid plasmids, (2) mixtures of adjacent
monomers from a cloned segment of this satellite DNA, (3) mixtures of
monomer units isolated by restriction nuclease cleavage of total
1-688 g/cc satellite DNA. Both direct sequence determination and
restriction nuclease cleavage indicate that certain positions in the
repeat can be highly variable with up to 50% of certain restriction
sites having altered recognition sequences. Despite the high degree
of variation at certain sites, most positions in the sequence are
highly conserved Sequence analysis of a mixture of 15 adjacent
monomer units detected only nine variable positions out of 359
base-pairs. Total satellite DNA showed only four additional
positions. While some variability would have been missed due to the
sequencing methods used, we conclude that the variation from one
repeat to the next is not random and that most of the satellite
repeat is conserved. This conservation may reflect functional aspects
of the repeated DNA, since we have shown earlier that part of this
sequence serves as a binding site for a sequence-specific DNA binding
protein isolated from Drosophila embryos (Hsieh & Brutlag,
1979).
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