Genes and non-coding DNA sequences

The DNA sequences of cloned complex satellite DNAs from Hawaiian Drosophila and their bearing on satellite DNA sequence conservation

A class of restriction endonuclease fragments near 185 bp in length and comprising approximately 20% of the genomes of 3 species of Hawaiian Drosophila has been cloned using bacteriophage M13. The nucleotide sequences of 14 clones have been determined and the variation between clones has been found to be due to deletions and base changes. Analyses of uncloned material show that the cloning system itself does not introduce the variation. The variation of the basic repeat within and between species is high; 15% due to deletions and 10% due to base changes. The Drosophila data are similar in many respects to both the 23 bp calf satellite results (Pech et al., 1979 b) and those from sequence analyses of the 170 bp primate restriction fragments (Rubin et al., 1979; Donehower et al., 1980, Wu and Manuelidis, 1980). The intraspecies level of base changes and deletions in the calf satellite approaches 25% as does that in the human/African green monkey/baboon comparisons. The between species variation in the primate group is near 35%. Direct sequencing methods thus reveal a widespread sequence heterogeneity in both invertebrate and mammalian satellite systems of long or short repeat length. This heterogeneity does not support the strict sequence conservation implied by the "library" hypothesis, which claims a functional role in speciation for the rigid conservation of satellite DNA sequences (Fry and Salser, 1977). Furthermore the Drosophila and primate data reveal that satellite DNAs can change rapidly, though nonrandomly, at the nucleotide sequence level in a relatively closely knit group such as the Hawaiian species, as well as in more distantly related species from amongst the primates. We draw two major conclusions. There is no universal attribute of satellite DNA sequence per se, the only biological variable to date being the amount of satellite DNA and its effect in the germ line. Many aspects of satellite DNA evolution conform to Kimura's (1979) concepts of neutrality.

Gene clusters and the HLA system

The major human histocompatibility, or HLA system, is now known to include a number of closely linked loci controlling cell surface specificities, components of the complement system and immune response. Three loci, HLA-A, B and C, control serological determinants found on nearly all cells; a fourth locus, HLA-D, codes for determinants controlling the mixed lymphocyte culture reaction that are present only on B lymphocytes and monocytes. The products of the HLA-A, B and C loci are very similar to each other, as expected if they have arisen by duplication from a common ancestor. The HLA-D products however, show no homology with these and each in turn is different from the complement components (C2, C4 and Bf) coded for in the HLA region. If this complex genetic region has arisen by a series of duplications, one must explain how four different structural gene products can arise from a single duplicated nucleic acid sequence. Different proteins could be translated from the same nucleotide sequence through the use either of different reading frames or of different, not necessarily adjacent, parts of a sequence in different combinations. It seems likely that the general organization of the genetic material of higher organisms is into clusters of duplicated genes like the HLA region and that the numbers of such clusters, rather than the number of individual genes, reflects the genetic complexity of higher organisms.