Imprinted genes and imprinting control regions show predominant intermediate methylation in adult somatic tissues

Abstract

Genomic imprinting is an epigenetic feature characterized by parent-specific monoallelic gene expression. The aim of this study was to compare the DNA methylation status of imprinted genes and imprinting control regions (ICRs), harboring differentially methylated regions (DMRs) in a comprehensive panel of 18 somatic tissues. The germline DMRs analyzed were divided into ubiquitously imprinted and placenta-specific DMRs, which show identical and different methylation imprints in adult somatic and placental tissues, respectively. We showed that imprinted genes and ICR DMRs maintain methylation patterns characterized by intermediate methylation levels in somatic tissues, which are pronounced in a specific region of the promoter area, located 200-1500 bp from the transcription start site. This intermediate methylation is concordant with gene expression from a single unmethylated allele and silencing of a reciprocal parental allele through DNA methylation. The only exceptions were seen for ICR DMRs of placenta-specific imprinted genes, which showed low levels of methylation, suggesting that these genes escape parent-specific epigenetic regulation in somatic tissues.

Keywords: ICR; Levene's test; genomic imprinting; methylation; somatic tissues.

Figure 1.. Visualization of beta-density and methylation level (vertical axis – beta-density (maximum value of 10) and horizontal axis – methylation level) for imprinted (A) and nonimprinted (B) genes, captured by methylation array.

Positive and negative controls are shown by blue and red lines, respectively. Each tissue is shown by a gray line. Imprinted genes have an increased number of intermediately methylated probes with beta-value in 0.5–0.7 range, if compared with nonimprinted genes, as shown in gray boxes.

Figure 2.. Visualization of probes with beta-value in range of 0.5–0.7 for imprinted genes and nonimprinted genes.

Promoter region TSS1500 has the highest ratio of intermediately methylated probes in imprinted genes, while the smallest difference was detected in TSS200, 5′UTR, the first exon and gene body regions. The asterisks define the differences of 22.8 and 34.2% for TSS1500 and 3′UTR, respectively, being the only significant results for this analysis. The TSS1500 promoter area of imprinted genes contains 22.8% more 0.5–0.7 β-value probes than nonimprinted genes (p = 6.57 × 10^-5). The 3′UTR area of imprinted genes has 34.2% less 0.5–0.7 β-value probes than nonimprinted genes (p = 6.2 × 10^-13). The differences in the TSS200, 5′UTR, the first exon and gene body were only 7.9, 7.3, 2.2 and 5.7% (p = 0.2128, p = 0.2578, p = 0.7929, and p = 0.338), respectively; being insignificant after multiple correction. TSS: Transcription start site.

Figure 3.. Visualized methylation patterns across 17 human somatic tissues for known germline ICR DMRs.

Positive and negative controls are shown by blue and red lines, respectively. Each tissue is shown by a gray line, whereas the mean of all tissues is shown by black line. The pattern specific for ubiquitously imprinted ICR DMRs is associated with increased number of intermediately methylated probes. While the placenta-specific ICR DMRs are associated with dominance of lowly methylated probes, except for GPR1-AS and MIR-512 genes for which unique patterns were observed (as explained in the text).