An Approach to Evolutionary Relationships of Mammalian DNA Viruses Through Analysis of the Pattern of Nearest Neighbor Base Sequences

DNA Methylation--A Regulatory Signal in Eukaryotic Gene Expression

“…The degree of methylation of C in these sequences varies greatly depending on many parameters, such as species, type of gene and stage of development. It may prove to be highly significant that the dinucleotide CpG occurs much less frequently in mammalian DNA than would be expected statistically (Subak-Sharpe et al, 1966).…”

Distinctive features of large complex virus genomes and proteomes

“…It was shown with few exceptions that small eukaryotic viral genomes (Յ30-kb genome size) are CpG suppressed (significantly underrepresented), generally to the same extent as the host genome (8,9,15,16). Small plant viruses are also inclined to be CpG suppressed.…”

“…For double-stranded DNA sequences, a symmetrized version { * XY } is calculated from frequencies of the sequence concatenated with its inverted complementary sequence. Our studies of DNA and genomic data have demonstrated that the dinucleotide relative abundance profiles { * XY } evaluated for disjoint 50-kb DNA contigs from the same organism are approximately constant throughout its genome and are generally more congruent to each other than they are to those from 50-kb contigs of different organisms (8)(9)(10)(11)(12). On this basis, we refer to the vector profile { * XY } of a given genome as its ''genomic signature'' diagnostic of different groups of organisms.…”

Sp1 transcription factor binds DNA and activates transcription even when the binding site is CpG methylated.

“…CpG is a rare dinucleotide in the DNA of higher eukaryotes (Subak-Sharpe et al 1966) and in the majority of CpGs the cytidine contains a 5-methyl group. Ten years ago it was observed that several CpG dinucleotides in the rabbit p-globin gene were methylated in tissues where the gene was inactive.…”