Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses?
Dinucleotide over- and underrepresentation is evaluated in all available completely sequenced DNA or RNA viral genomes, ranging in size from 3 to 250 kb (available RNA viruses fall into the small-virus category). The dinucleotide CpG is statistically underrepresented (suppressed) in all but four of the small viruses (more than 75 with lengths of < 30 kb) but has normal relative abundances in most large viruses (> or = 30 kb). Most retrotransposons in eukaryotic species also show low CpG relative abundances. Interpretations, especially in some cases of DNA viruses or viruses with a DNA intermediate, might relate to methylation effects and modes of viral integration and excision. Other possible contributing factors relate to dinucleotide stacking energies, special mutation mechanisms, and evolutionary events.
Karlin
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Department of Mathematics, Stanford University, California 94305.
Doerfler
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Cardon
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D001120:Arginine / Q000235:genetics; D001482:Base Composition; D005075:Biological Evolution; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004251:DNA Transposable Elements / Q000235:genetics; D004267:DNA Viruses / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics*; D015226:Dinucleoside Phosphates / Q000235:genetics*; D005057:Eukaryotic Cells / Q000382:microbiology; D016679:Genome, Viral; D008970:Molecular Weight; D010942:Plant Viruses / Q000235:genetics; D012328:RNA Viruses / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D013489:Suppression, Genetic; D016662:Virus Integration; D014780:Viruses / Q000235:genetics*
D001120:Arginine; D004262:DNA Restriction Enzymes; D004251:DNA Transposable Elements; D004279:DNA, Viral; D015226:Dinucleoside Phosphates; D012367:RNA, Viral; C015772:CpG dinucleotide