My lab focuses on understanding the mechanism of genomic imprinting. Genomic imprinting is a mammalian-specific phenomenon whereby the expression of a subset of genes depends on their parental origin. In other words, although we inherit one copy of every gene from our mothers and one copy from our fathers, there are a small number of genes for which only the maternally inherited copy is expressed and a small number for which only the paternally inherited copy is expressesd. There are two major consequences of this unusual form of gene regulation. First, mutations in imprinted genes act in a dominant, parent of origin-specific fashion since there is not a second copy whose wild-type expression can compensate for the mutation. Second, every mammal needs to have a genetic contribution from both a male and a female parent – otherwise, genes critical for normal development will not be expressed. Failure to achieve genomic imprinting can result in developmental disorders such as Beckwith-Wiedemann, Prader-Willi and Angelman syndromes.

One main question in the field of genomic imprinting is: how does the cellular machinery distinguish the maternally inherited allele from the paternally inherited allele so that it knows which copy should be expressed and which copy should remain silent? The simple answer is that the maternal and paternal alleles must be marked so that they appear to be different from each other. To date, the best candidate for the imprinting mark is DNA methylation. In mammals, DNA methylation is a modification of cytosines that are present in CG dinucleotides, such that the cytosines have a methyl group covalently attached at the 5′ position. This type of modification is called epigenetic because it is a modification of the DNA structure but does not alter the DNA sequence. The reason DNA methylation stands out as a candidate for the imprinting mark is that most imprinted genes are associated with a region of differential methylation – for example, the silent paternal allele of an imprinted gene may be methylated while the expressed maternal allele is unmethylated.

As mentioned above, all imprinted genes are associated with a primary region of differential DNA methylation which serves as an imprinting control region. However, the precise regulation of imprinted genes requires additional epigenetic modifications, including secondary differentially methylated regions (DMRs) and differential distribution of modified histones on the parental alleles, or copies, of imprinted genes. Secondary DMRs are regions at which differential methylation is not inherited via the gamete; rather, allele-specific methylation at secondary DMRs is acquired post-fertilization. One aspect of my research is focused on understanding when methylation is acquired during embryogenesis, and how these secondary DMRs differ from primary imprinting control regions. To do this, my lab conducts analysis of DNA methylation patterns at imprinted genes during various stages of development in the mouse. During our analyses, we observed that DNA methylation displays a high level of asymmetry on the complementary strands of secondary DMRs; this result was unexpected because the enzyme that maintains DNA methylation typically functions with very high fidelity. To understand the biochemical basis of this hemimethylation, we examined these sequences for 5-hydroxymethylcytosine, an oxidized form of methylated cytosine as this chemical modification could interfere with maintenance methylation and could also lead to further oxidation and removal of the methylated base. We found enrichment of 5-hydroxymethylcytosine at some, but not all, of the secondary DMRs we analyzed and are currently conducting a more comprehensive analysis in order to examine more potentially methylated residues at each sequence.

The high level of hemimethylation we observed at secondary DMRs should, over time, lead to reduced levels of methylation. However, when we examine DNA methylation patterns across development, overall methylation levels are stable. Therefore, we propose that secondary DMRs must be continuously remethylation in order to maintain their methylated status. We are currently initiating a project to test this hypothesis.

Our research is currently funded by a grant from the National Science Foundation. Past research has been funded by the NSF, the National Institutes of Health, and Bryn Mawr College.

If you are a Bryn Mawr student who finds this work interesting, please feel free to contact me as there are opportunities for student research in my lab during the course of the academic year as well as in the summer.