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 availab le 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 <3 0 kb) but has normal relative abundances in most large viruses (greate r than or equal to 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 r elate to methylation effects and modes of viral integration and excisi on. Other possible contributing factors relate to dinucleotide stackin g energies, special mutation mechanisms, and evolutionary events.