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PLoS One. 2016 Jan 13;11(1):e0146402. doi: 10.1371/journal.pone.0146402. eCollection 2016.
Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily Conserved.
Zhang M1,2,
Wang CC3,
Yang C1,
Meng H1,2,
Agbagwa IO4,
Wang LX3,
Wang Y3,
Yan S3,
Ren S5,
Sun Y5,
Pei G6,7,
Liu X1,
Liu J8,
Jin L3,
Li H3,
Sun Y1.
- 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.
Fig 1Characteristics of the Y chromosome and the Y chromosome phylogenetic tree.
A) The abridged general view of stable inheritance of the Y chromosome among male generations. Recombination between homologous chromosomes are existed in other chromosomes. B) Illustration diagram of the SNP inheritance on the Y chromosome. Each color star represents a new SNP, and it can be inherited to the next generation. C) The abbreviated form of the Y chromosome phylogenetic tree. Haplogroup E and O were selected for this study. D) The tree of haplogroup O and its subgroups in Han Chinese population. The methylation patterns of bold labeled subclades are studied.
PLoS One. 2016;11(1):e0146402.
Fig 2The conservative DNA methylation pattern on the Y chromosome within three haplogroup O2* families.
A) Pedigree showing the relationship of family members. B) Heat map showing the methylation level of the Y chromosome in each sample. Each row line represents a single tested site, with each vertical line showing the β-value obtained in each individual sample. DNA methylation level is colored from orange to red to indicate low to high. C) The DNA methylation level is shown around the annotated genes and CpG Islands of the Y chromosome. D) Bar graphs showing the distribution of hyper-, intermediate-, and hypo-methylation sites on the Y chromosome in each sample respectively. Red indicates the hyper-methylation sites (β-value > 0.8), blue indicates intermediate-methylation sites (β-value: 0.2 to 0.8), and green indicates hypo-methylation sites (β-value < 0.2).
PLoS One. 2016;11(1):e0146402.
Fig 3The similar DNA methylation pattern on the Y chromosome among different geographic subgroups of haplogroup O2*.
A) Geographic distribution of 28 haplogroup O2* individuals. B) Heat map showing the methylation level of the Y chromosome in each sample. Each row line represents a single site, with each vertical line showing the β-value obtained in each individual sample. DNA methylation level is colored from orange to red to indicate low to high. C) The DNA methylation level is shown around the annotated genes and CpG Islands of the Y chromosome. D) Bar graphs showing the distribution of hyper-, intermediate-, and hypo-methylation sites on the Y chromosome in each haplogroup O2* sample.
PLoS One. 2016;11(1):e0146402.
Fig 4Haplogroup-specific DNA methylation variation in haplogroup O3a2b samples.
A) The information of Y haplotype and coalescence time for samples. The left bar graph indicates the coalescence time, from 27 thousand years ago (kya) to now. Numbers in red indicate the coalescence time (in years) and 95% confidence interval of the node. B) Heat map showing the Pearson correlation coefficients among different haplogroups. Correlation coefficients are colored yellow to red to indicate low to high, respectively. C) Box plots showing the haplogroup O3a2b-specific methylation sites. **P < 0.01. D) The methylation level of cg07765982 and cg13365400 within all samples. Each data point represents the β-value of each sample.
PLoS One. 2016;11(1):e0146402.
Fig 5The methylation pattern of functional regions on the Y chromosome.
A) Box plots showing the standard deviation of methylation level within each region. The median line indicates the average methylation level, the edges represent the 25th/75th percentile, and the whiskers represent the 2.5th/97.5th percentile. B−D). Heat map showing the methylation levels of 38 detected TSS1500 regions (B), 53 gene body regions (C), and 55 CpG island regions (D).
PLoS One. 2016;11(1):e0146402.
Fig 6The different methylation site in haplogroup E1b1a1 samples.
A) The Y chromosome phylogenetic tree showing the coalescence time between haplogroup E and haplogroup O. Numbers in red indicate the coalescence time (in years) and 95% confidence interval of the node. B) Box plots showing the methylation level of haplogroup E1b1a1-specific methylation site. **P < 0.01. C) The methylation level of cg05782707 among all samples. Each data point represents the β-value of each sample. D) The genomic location of cg05782707 site.
PLoS One. 2016;11(1):e0146402.
Fig 7The inheritance schematic model of the DNA methylation pattern on the Y chromosome.
A) Illustration model of the SNP inheritance on the Y chromosome. Each color star represents a new SNP, and it can be inherited to the next generation. B) The inheritance schematic model of DNA methylation pattern on the Y chromosome. Red star indicates a haplogroup-specific methylation site. This model shows the stable methylation pattern on the Y chromosome within each haplogroup. White circles represent unmethylated sites, black circles represent the methylated sites. Numbers in red indicate the coalescence time (in years) and the 95% confidence interval of the node.
PLoS One. 2016;11(1):e0146402.
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