Summer Science Research
Methylation Patterns Upstream of the Rasgrf1 DMR
A small fraction of mammalian genes is regulated by genomic imprinting. Genes that are regulated in this manner are expressed in a parent-of-origin-specific manner. This trend makes imprinted genes unique, because while most other genes express both a maternally and paternally derived allele, imprinted genes express only one of the two alleles. The mechanisms that achieve this expression are DNA methylation and histone modification, which cause a favored expression of either the maternal or paternal allele. As a whole, genomic imprinting falls under the broader category of epigenetics, which describes the modes of gene regulation that do not fall under sequence-based regulation.
One of the largest questions present in the field of imprinting is the question of how particular loci are able to attract imprinting machinery. As an effort to address this question, there are ongoing studies looking into the DNA methylation patterns and histone modifications associated with particular regions that are known to be imprinting control regions – or ICRs. This understanding is crucial, because it may help to address developmental disorders and disease associated with a failure to achieve and maintain proper methylation and/or histone modifications.
Rasgrf1 belongs to the subset of imprinted genes. It functions as a guanine nucleotide exchange factor, converting GDP to GTP. It is also part of the minority of paternally-methylated imprinted genes. The methylation of Rasgrf1 not only marks its parental origin, but is also required for monoallelic expression of the gene in brain tissue. Unlike most DNA methylation which causes gene silencing, the methylation associated with Rasgrf1 is permissive, meaning that the methylated allele is expressed. In Rasgrf1, the differentially methylated region (DMR) lies approximately 30 kb upstream of the gene’s promoter. Further upstream is an enhancer, which can be blocked by the enhancer-blocking protein CTCF. When the region upstream of the promoter is methylated (as in the paternal allele), the enhancer-blocker cannot bind and transcription is able to proceed, which is why the methylated allele is the expressed allele.
The parameters of the Rasgrf1 DMR have been roughly established, but new evidence suggests that the DMR for Rasgrf1 extends farther than previously believed. Further study is warranted to determine whether the methylation upstream of the DMR – termed the uDMR – has continuous or fragmented methylation patterns. In order to examine the methylation status of the uDMR, four tissues from 5 day old mice are to be examined – including the brain and liver (monoallelic) as well as the lung and kidney (biallelic). By defining the extent of the DMR in Rasgrf1 more precisely, studies conducted on histone modifications in this region will thus be expanded accordingly.