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The third, or wobble, position of codons provides a high degree of possible degeneracy and is an elegant mechanism of fault tolerance. Previously, nucleotide biases between organisms at the wobble position have been documented and correlated with abundance of the complimentary tRNAs. We, as well as others, have noticed a bias for cytosine and guanine at this third position in a subset of transcripts within a single organism. The bias is present in some plant species, warm-blooded vertebrates but not all plants, nor invertebrates nor cold-blooded vertebrates. Here we demonstrate that within certain organisms the abundance of GC at the wobble position (GC3) can be used to distinguish two classes of genes. These classes of genes differ in gene expression, CpG methylation sites and number of paralogs. Together this evidence suggests that the genes with high levels of GC3 represent a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. Either explanation suggests these are an important class of genes to examine in biological systems.
BMC Genomics full text paper: