Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily Conserved

Minjie Zhang; Chuan-Chao Wang; Caiyun Yang; Hao Meng; Ikechukwu O Agbagwa; Ling-Xiang Wang; Yingzhi Wang; Shi Yan; Shancheng Ren; Yinghao Sun; Gang Pei; Xin Liu; Jiang Liu; Li Jin; Hui Li; Yingli Sun

doi:10.1371/journal.pone.0146402

Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily Conserved

PLoS One. 2016 Jan 13;11(1):e0146402. doi: 10.1371/journal.pone.0146402. eCollection 2016.

Authors

Minjie Zhang^{1

2}, Chuan-Chao Wang³, Caiyun Yang¹, Hao Meng^{1

2}, Ikechukwu O Agbagwa⁴, Ling-Xiang Wang³, Yingzhi Wang³, Shi Yan³, Shancheng Ren⁵, Yinghao Sun⁵, Gang Pei^{6

7}, Xin Liu¹, Jiang Liu⁸, Li Jin³, Hui Li³, Yingli Sun¹

Affiliations

¹ Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
² University of Chinese Academy of Sciences, Beijing, 100049, China.
³ State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
⁴ Department of Plant Science & Biotechnology, University of Port Harcourt, Port Harcourt, Nigeria.
⁵ Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China.
⁶ State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
⁷ Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, 200092, China.
⁸ Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.

Abstract

DNA methylation plays an important role for mammalian development. However, it is unclear whether the DNA methylation pattern is evolutionarily conserved. The Y chromosome serves as a powerful tool for the study of human evolution because it is transferred between males. In this study, based on deep-rooted pedigrees and the latest Y chromosome phylogenetic tree, we performed epigenetic pattern analysis of the Y chromosome from 72 donors. By comparing their respective DNA methylation level, we found that the DNA methylation pattern on the Y chromosome was stable among family members and haplogroups. Interestingly, two haplogroup-specific methylation sites were found, which were both genotype-dependent. Moreover, the African and Asian samples also had similar DNA methylation pattern with a remote divergence time. Our findings indicated that the DNA methylation pattern on the Y chromosome was conservative during human male history.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosomes, Human, Y / genetics*
Conserved Sequence*
DNA Methylation / genetics
Epigenesis, Genetic*
Evolution, Molecular*
Family
Geography
Haplotypes / genetics
Humans
Inheritance Patterns / genetics
Male
Models, Genetic
Phylogeny
Time Factors

Grants and funding

This work was supported by Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDA01040407), National Natural Science Foundation of China (grant no. 91019024, grant no. 31100558, and grant no. 91131002), National Basic Research Program of China (973 Program, grant no. 2012CB518302, and grant no. 2013CB911001), National Excellent Youth Science Foundation of China (grant no. 31222030), Shanghai Rising-Star Program (grant no. 12QA1400300), China Ministry of Education Scientific Research Major Project (grant no. 311016 and 113022A), MOE University Doctoral Research Supervisor’s Funds (grant no. 20120071110021), and Shanghai Professional Development Funding (grant no. 2010001).