Allele-specific Methylation of Imprinted Genes in Fetal Cord Blood is Influenced By Cis-Acting Genetic Variants and Parental Factors

Figures & data

Figure 1.  Correlation of paternal and maternal age, respectively, with fetal cord blood methylation of the paternal and maternal alleles.

The upper panel shows three paternally imprinted/methylated (H19 IG DMR, IGF2 DMR0 and MEG3 IG DMR) regions and the lower panel shows three maternally imprinted/methylated (MEST, NNAT and PEG3) amplicons. Each dot represents an informative FCB sample. Regression lines indicate the direction of age-related changes.

FCB: Fetal cord blood; IG DMR: Intergenic differentially methylated region.

Figure 2.  Effect of paternal BMI on paternal MEST allele methylation.

The left diagram shows identical BMI effects on paternal allele methylation in female and male FCBs. The right diagram displays the impact of the underlying genetic variation (A vs G SNP) on paternal MEST methylation.

FCB: Fetal cord blood.

Table 1.  SNP haplotype effects on the allele-specific methylation of imprinted genes.

Gene	Parental allele in FCB	Sample size	SNP effects (G over A) on methylation
			Estimate	St. error	p-value
H19 IG DMR	Methylated (paternal)	46	-0.033	0.013	0.013
	Unmethylated (maternal)	46	0.018	0.005	0.001
IGF2 DMR0	Methylated (paternal)	46	-0.023	0.009	0.023
	Unmethylated (maternal)	46	-0.045	0.010	<0.0001
MEG3 IG DMR	Methylated (paternal)	44	0.002	0.007	0.732
	Unmethylated (maternal)	44	-0.009	0.014	0.494
MEST (PEG1)	Methylated (maternal)	46	-0.034	0.009	0.001
	Unmethylated (paternal)	46	0.113	0.013	<0.0001
NNAT (PEG5)	Methylated (maternal)	39	0.032	0.006	<0.0001
	Unmethylated (paternal)	39	-0.102	0.018	<0.0001
PEG3	Methylated (maternal)	46	-0.006	0.003	0.035
	Unmethylated (paternal)	46	0.004	0.002	0.059

FCB: Fetal cord blood.

Figure 3.  SNP effects on allele-specific methylation of the maternally imprinted MEST promoter and the paternally imprinted MEG3 IG DMR.

For each gene, the upper panel shows single CpG methylation levels of the methylated allele and the lower panel of the unmethylated allele. A (Adenine) alleles are indicated by blue and G (Guanine) alleles by red dots. All 32 CpGs in the MEST target region display a clear SNP effect. Maternally methylated A alleles consistently show a higher methylation than maternally methylated G alleles, whereas paternally unmethylated A alleles show a lower methylation than paternally unmethylated G alleles. In contrast, none of the 8 targeted CpGs in the MEG3 IG DMR displays a clear SNP effect.

IG DMR: Intergenic differentially methylated region; SNP: Single nucleotide polymorphism.

Figure 4.  Parental allele-specific epimutation rates of the paternally imprinted H19 IG DMR, IGF2 DMR0 and MEG3 IG DMR and the maternally imprinted MEST, NNAT and PEG3 DMRs in fetal cord blood samples.

Blue and red dots indicate the epimutation rates on the unmethylated and methylated alleles, respectively, for a given gene and sample.