Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels --Supplementary information: source code, supplementary file and links to data
Abstract
Different human genes often exhibit different degrees of robustness or stability in their DNA methylation levels between tissues, samples or cell types. This may be related to the evolution of the human genome. Thus, we compared the evolutionary conservation between two types of genes: genes with stable DNA methylation levels (SM genes) and genes with fluctuant DNA methylation levels (FM genes). For long-term evolutionary characteristics between species, we compared the percentage of the orthologous genes, evolutionary rate dn/ds and protein sequence identity. We found that the SM genes had a greater percentage of the orthologous genes, lower dn/ds, and a higher protein sequence identity in all the 21 species. These results indicated that the SM genes were more evolutionarily conserved than the FM genes. For short-term evolutionary characteristics among human populations, we compared the single nucleotide polymorphism (SNP) density, and the linkage disequilibrium (LD) degree in HapMap populations and 1000 genomes project populations. We observed that the SM genes had a lower SNP densities, and a higher degree of LD in all the 11 HapMap populations and 13 1000 genomes project populations. These results mean that the SM genes had more stable chromosome genetic structures, and were more conserved than the FM genes.