Estimation of the Equilibrium GC Content of Human Genome

Although the GC content of the human genome is known, it remains undecided whether the base composition is already in equilibrium. This study aimed to examine the equilibrium GC content of the human genome based on 2,504 genomes from the 1000 Genomes Project. By recreating the results of some previous research on genome analysis, we revealed the problems in the results of those studies and the causes of the problems. The present results indicate that the GC content of the human genome has not yet reached equilibrium, and it is evolving toward a higher GC content. Furthermore, by analyzing the quantitative changes in CpG dinucleotides before and after mutations, we found that the effect of methylation on the GC content of a genome is very limited, even leading to an increase in the GC content of the genome rather than only a decrease. These findings, therefore, contradict the traditional perception.