title: Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels.
abstract: Different human genes often exhibit different degrees of stability in their DNA methylation levels between tissues, samples or cell types. This may be related to the evolution of 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 greater percentages of the orthologous genes, lower dn/ds, and higher protein sequence identities 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 lower SNP densities, and higher degrees 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.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Ruijie
authors.initials: R
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Wenhua
authors.initials: W
authors.lastname: Lv
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Meiwei
authors.initials: M
authors.lastname: Luan
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Jiajia
authors.initials: J
authors.lastname: Zheng
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Miao
authors.initials: M
authors.lastname: Shi
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Hongjie
authors.initials: H
authors.lastname: Zhu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Hongchao
authors.initials: H
authors.lastname: Lv
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Zhenwei
authors.initials: Z
authors.lastname: Shang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Lian
authors.initials: L
authors.lastname: Duan
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Yongshuai
authors.initials: Y
authors.lastname: Jiang
mesh_terms: D019175:DNA Methylation; D019143:Evolution, Molecular; D063990:Gene Ontology; D005796:Genes / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide
keywords: DNA methylation stability; SNP density; evolutionary characteristics; linkage disequilibrium