Fig 1.
Characteristics 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.
Fig 2.
The 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).
Fig 3.
The 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.
Fig 4.
Haplogroup-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.
Fig 5.
The 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).
Fig 6.
The 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.
Fig 7.
The 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.