Heterogeneity of genomes: measures and values.
Genomic homogeneity is investigated for a broad base of DNA sequences in terms of dinucleotide relative abundance distances (abbreviated delta-distances) and of oligonucleotide compositional extremes. It is shown that delta-distances between different genomic sequences in the same species are low, only about 2 or 3 times the distance found in random DNA, and are generally smaller than the between-species delta-distances. Extremes in short oligonucleotides include underrepresentation of TpA and overrepresentation of GpC in most temperate bacteriophage sequences; underrepresentation of CTAG in most eubacterial genomes; underrepresentation of GATC in most bacteriophage; CpG suppression in vertebrates, in all animal mitochondrial genomes, and in many thermophilic bacterial sequences; and overrepresentation of GpG/CpC in all animal mitochondrial sets and chloroplast genomes. Interpretations center on DNA structures (dinucleotide stacking energies, DNA curvature and superhelicity, nucleosome organization), context-dependent mutational events, methylation effects, and processes of replication and repair.
Karlin
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S
Department of Mathematics, Stanford University, CA 94305-2125.
Ladunga
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I
Blaisdell
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BE
D000818:Animals; D001482:Base Composition; D004247:DNA / Q000737:chemistry*; D004269:DNA, Bacterial / Q000737:chemistry; D004271:DNA, Fungal / Q000737:chemistry; D005057:Eukaryotic Cells; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D017422:Sequence Analysis, DNA / Q000379:methods*
D004269:DNA, Bacterial; D004271:DNA, Fungal; D009838:Oligodeoxyribonucleotides; D004247:DNA