Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels

Ruijie Zhang; Wenhua Lv; Meiwei Luan; Jiajia Zheng; Miao Shi; Hongjie Zhu; Jin Li; Hongchao Lv; Mingming Zhang; Zhenwei Shang; Lian Duan; Yongshuai Jiang

doi:10.18632/oncotarget.5504

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Research Papers:

Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels

Ruijie Zhang _, Wenhua Lv, Meiwei Luan, Jiajia Zheng, Miao Shi, Hongjie Zhu, Jin Li, Hongchao Lv, Mingming Zhang, Zhenwei Shang, Lian Duan and Yongshuai Jiang

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Oncotarget. 2015; 6:40235-40246. https://doi.org/10.18632/oncotarget.5504

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Abstract

Ruijie Zhang1,*, Wenhua Lv1,*, Meiwei Luan1,*, Jiajia Zheng1,*, Miao Shi1,*, Hongjie Zhu1, Jin Li1, Hongchao Lv1, Mingming Zhang1, Zhenwei Shang1, Lian Duan1, Yongshuai Jiang1

1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China

*These authors have contributed equally to this work

Correspondence to:

Yongshuai Jiang, e-mail: [email protected]

Ruijie Zhang, e-mail: [email protected]

Keywords: DNA methylation stability, evolutionary characteristics, SNP density, linkage disequilibrium

Received: July 26, 2015 Accepted: October 06, 2015 Published: October 19, 2015

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.

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Research Papers:

Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels

Abstract