Comparative Anatomy of Chromosomal Domains with Imprinted and Non-Imprinted Allele-Specific DNA Methylation

Abstract

Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.

DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition

“…We examined whether early life malnutrition was associated with DNA methylation changes in regions that show parent-of-origin specific DNA methylation patterns. We observed that several nutrition-associated DMR loci in our study occurred at known or putative imprinted genes, including L3MBTL1, MEST / MESTIT1, JAKMIP1 , and VTRNA2-1 (28–30). In total, 73 of the 1000 autosomal probes that showed a significant difference in methylation levels between MAL and CON G1 individuals correspond to regions that exhibit a parent-of-origin bias in DNA methylation levels, representing a highly significant 40.6 fold enrichment when compared to the non-imprinted genomic regions (p=3.5×10 −91 ) (Supplemental Table S12).…”

Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function

“…2b. Five DMRs have previously been reported by others: Two regions (DMR87 and DMR134) overlap previously designated hap-ASM DMRs [2], two DMRs contain a previously reported SNP mQTL (DMR25—rs6760544 [5], and DMR104—rs11158727 [6]), and one DMR contains a previously reported ASM–SNP (DMR24—rs1530562 [14]). The majority of the DMRs are either intergenic (79/157) or intronic (57/157), while 13/157 span over an exon–intron boundary and 7/157 are located within an exon (Additional file 4).…”

Heritable methylation marks associated with breast and prostate cancer risk

“…Some transgenerationally heritable DNA methylation marks have been associated with nearby genetic variation but allele‐specific methylation at VTRNA2‐1 has not yet been linked to any underlying genetic variation . This suggests that the allele‐specific methylation pattern at VTRNA2‐1 is unlikely to be an mQTL and further supports polymorphic epigenetic imprinting of the region.…”