No Evidence for a Parent-of-Origin Specific Differentially Methylated Region Linked to RASGRF1

Abstract

Imprinted genes are expressed from one parental allele in a parent-of-origin manner. This monoallelic behavior is regulated by allele-specific DNA methylation that is confined to differentially methylated regions (DMRs). To date there are over 80 known human imprinted genes of which only three are known to have paternally methylated DMRs. In mice there exists an additional paternally methylated DMR associated with Rasgrf1. The Rasgrf1 gene forms part of the MAPK signaling pathway and plays a role in long-term memory formation and growth control. A RASGRF1-associated parent-of-origin specific DMR in humans and its methylation status in sperm DNA have not been explored. The primary aim of this study was to determine whether the human RASGRF1 gene contains a DMR and whether this DMR is paternally methylated and shows roughly 50% methylation in somatic tissue. Computational assessments were done to identify putative CTCF binding sites, CpG islands (CGIs) that could serve as potential RASGRF1 DMRs and tandem repeats within or adjacent to these CGIs. The methylation status of three putative CGIs was assessed using quantitative pyrosequencing technology. None of the putative CTCF binding sites was found to occur in the predicted CGIs. The three putative CGIs linked to RASGRF1 did not display allele-specific methylation. While one of the three CGIs was found to be hypomethylated in both blood DNA and sperm DNA, the other two were found to be hypermethylated. The CGIs evaluated in this study did not fit the criteria of being a allele-specific DMR. Unlike the mouse Rasgrf1 locus, the human RASGRF1-associated CpG rich regions do not exhibit differential methylation in a parent-of-origin manner.

Grandmothers’ smoking in pregnancy is associated with a reduced prevalence of early-onset myopia

“…This guanine nucleotide exchange factor is an important regulator of intracellular signaling and neural plasticity in the brain. Clearly showing genomic imprinting in rodents and pigs, with brain expression only from the paternally-derived chromosome, there is uncertainty about the imprinting status of the RASGRF1 gene in humans 41,42 . A more recent study found that there are more imprinted domains in the human placenta than in somatic tissues, and found RASGRF1 to be paternally expressed in human placenta and that this is controlled by a maternally methylated DMR 43 .…”

Role of Mammalian DNA Methyltransferases in Development

“…In addition, DNMT3C, the recently discovered de novo DNMT essential for male mice fertility, is not present in human genome (5). Consistently, RASGRF1 in humans does not contain a paternally methylated region like in mice (122), whereas DNMT3C is responsible for establishing the DNA methylation imprint at this locus during spermatogenesis (5).…”

Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children

“…Given that an equivalent alternative promoter of human ZDBF2 has not yet been described and the nature of the imprint at this locus remains unclear, we excluded this locus from our analysis. The Rasgrf1 ICR is paternally methylated in mice, but its status as an imprinted locus in humans is debated ( Pitamber et al. 2012 ; Yuen et al.…”