Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs): paternally methylated DMRs contain less CpGs than maternally methylated DMRs

Abstract

Imprinted genes in mammals show monoallelic expression dependent on parental origin and are often associated with differentially methylated regions (DMRs). There are two classes of DMR: primary DMRs acquire gamete-specific methylation in either spermatogenesis or oogenesis and maintain the allelic methylation differences throughout development; secondary DMRs establish differential methylation patterns after fertilization. Targeted disruption of some primary DMRs showed that they dictate the allelic expression of nearby imprinted genes and the establishment of the allelic methylation of secondary DMRs. However, how primary DMRs are recognized by the imprinting machinery is unknown. As a step toward elucidating the sequence features of the primary DMRs, we have determined the extents and boundaries of 15 primary mouse DMRs (including 12 maternally methylated and three paternally methylated DMRs) in 12.5-dpc embryos by bisulfite sequencing. We found that the average size of the DMRs was 3.2 kb and that their average G+C content was 54%. Dinucleotide content analysis of the DMR sequences revealed that, although they are generally CpG rich, the paternally methylated DMRs contain less CpGs than the maternally methylated DMRs. Our findings provide a basis for the further characterization of DMRs.

MIRA-SNuPE, a quantitative, multiplex method for measuring allele-specific DNA methylation

“…The U2af1 SNP in the 16-plex 44 assay lies at the outside boundary of the U2af1 DMR, and although it is suitable to discern allele-specific chromatin features associated with the U2af1 DMR, 44 it does not map to an area of the actual differential CpG methylation. Other known SNPs that map to the DMR are embedded in repeat elements, 12 and cannot be used in SNuPE assays. The paternal allele was strongly overrepresented in the MIRA fraction at each paternally methylated DMR, the H19/Igf2 ICR, the Rasgrf1 DMR and the IG-DMR (Fig.…”

“…1A). Gamete-specific DNA methylation marks are established at paternally or maternally methylated germ line DMRs 12,13 in the male ©2 0 1 1 L a n d e s B i o s c i e n c e .…”

Very Small Embryonic/Epiblast-Like Stem Cells (VSELs) Residing in Adult Tissues and Their Role in Tissue Rejuvenation and Regeneration

“…So far, 15 primary DMRs have been identified in the mouse genome. Interestingly, most DMRs are methylated at the maternal allele and only three DMRs (at Igf2-H19, Rasgrf1, and Meg3 loci) are paternally methylated (Kobayashi et al, 2006). In addition to DNA methylation of DMRs, histone modifications also contribute to monoallelic expression of imprinted genes (Fournier et al, 2002;Mager et al, 2003).…”

Epigenetic asymmetry in the zygote and mammalian development

“…Specifically, ICRs are elements of up to several kilobases in size that are rich in CpG dinucleotides. Many correspond to CpG islands (Hutter et al, 2006;Kobayashi et al, 2006). At most ICRs, the allelic methylation is established during oogenesis.…”