Mentor: Tamara Davis
Genomic imprinting is a relatively rare phenomenon that occurs when one copy of a gene is expressed while the other copy remains silent in a parent-of-origin-specific manner. This process is often controlled by epigenetic factors, such as DNA methylation and histone modification, which alter the structure of DNA and influence gene expression. Understanding the regulation of imprinted gene expression is critical because without the proper control of genomic imprinting, severe developmental disorders, such as Prader-Willi Syndrome and Angelman Syndrome, may occur.
The majority of imprinted genes are expressed from the same allele in all tissue types, however, some imprinted genes display what is known as tissue-specific imprinting, which occurs when gene expression is monoallelic in some tissues yet biallelic in others. As the factors responsible for tissue-specific imprinting have not yet been identified, analysis of epigenetic markers on these imprinted genes will likely be critical to understanding this complex process. One particular tissue-specific imprinted gene, Rasgrf1, is paternally methylated in all tissues yet is expressed differentially across tissue types, which suggests that DNA methylation is not solely responsible for the tissue-specific imprinting of Rasgrf1. In the Davis lab, I will investigate whether modified histones are an important factor in regulating expression of Rasgrf1 by studying the distribution of various modified histones in two different regions on both alleles in mouse tissues with monoallelic expression, including liver and brain. In particular, we expect that the types of modifications present in the promoter region of the maternal and paternal alleles will be reflective of the relative expression levels of each allele such that permissive modifications will be present on the expressed paternal allele and repressive modifications will be present on the silent maternal allele. Furthermore, while DNA methylation at the imprinting control region is often associated with repressive histone modifications, it remains unclear whether this is true of Rasgrf1 in both monoallelic and biallelic tissues.
To investigate these questions, we will use chromatin immunoprecipitation (ChIP) to isolate chromatin containing specific modified histones. Using allele specific primers designed based on strain specific SNPs, we will then conduct allele specific quantitative PCR on the immunoprecipitated chromatin fractions to determine the relative levels of maternal and paternal alleles containing the modifications of interest at the promoter, DMR, and uDMR. Using this data, we will be able to determine whether histone modifications at various regions of Rasgrf1 are correlated with expression levels in a tissue and allele specific manner, which may provide insight into the role of histone modification in the tissue-specific imprinting of Rasgrf1.