Nicole Hamagami

Dr. Tamara Davis

Genomic imprinting is a mammalian specific epigenetic mechanism that facilitates the genetic expression of one parental allele over the other. Epigenetic factors such as DNA methylation and histone modifications function to regulate these expression states by attracting or repelling various elements required for DNA transcription. Differential distribution of such epigenetic modifications on the parental alleles therefore results in the differential expression of the two alleles. Specifically, posttranslational histone modifications structurally alter the chromatin itself or regulate enzymatic chromatin binding factors that play a role in genetic expression and imprinting.

Imprinted genes are important for normal development and failure to achieve genomic imprinting can lead to various genetic disorders. This knowledge has led to the identification of approximately 120 genes that undergo genomic imprinting. The study of imprinted genes is therefore crucial in better understanding the mechanisms behind gene inheritance, embryonic development, and specific genetic disorders such as Angelman syndrome and Prader-Willi syndrome.  The Davis Lab currently does research on the imprinted mouse gene Rasgrf1, which is paternally expressed in a tissue-specific manner. Previous studies in our lab investigating DNA methylation patterns across mono-allelic and bi-allelic tissues at the Rasgrf1 gene has shown that DNA methylation is present on the paternal allele in tissues with both imprinted and non-imprinted expression, indicating that DNA methylation cannot be the only modification responsible for the tissue-specific expression patterns observed at this gene locus.

Histone modifications are additional epigenetic factors that may explain the tissue-specific imprinted expression seen at the Rasgrf1 gene because some histone modifications are associated with gene expression while others are associated with gene silencing. Therefore, we want to determine whether these histone modifications have different patterns of distribution between mono- and bi-allelic tissues that could describe the tissue-specific expression patterns we see. My research specifically focuses on the relationship between histone modification distribution and differentiated gene expression in bi-allelic tissues. We have developed a specific assay consisting of a procedure known as chromatin immunoprecipitation (ChIP) coupled with allele-specific amplification of DNA using quantitative PCR to locate modified histones that are preferentially distributed on either or both parental alleles. In particular, our regions of analysis will focus on the promoter and a differentially methylated regulation region (DMR) of the Rasgrf1 gene. Since the chromatin structure at the promoter tends to reflect the expression patterns of the gene itself, we expect to see permissive and repressive histone modifications on the promoter region of the paternal and maternal chromosomes, respectively, in mono-allelic tissues, whereas we expect to see permissive modifications on both alleles for bi-allelic tissues. However, we are unsure how these modified histones will be distributed at the DMR site. The silencing nature of DNA methylation on the paternal allele may promote similarly repressive histone modifications on the methylated paternal allele and permissive histone modifications on the methylated maternal allele. If the modified histone distribution appears to reflect that of DNA methylation at these regions, then we may conclude that histone modifications are not involved in the differential expression seen in mono-allelic and bi-allelic tissues. Differences in distribution in mono-allelic versus bi-allelic tissues, however, may suggest the involvement of these modified histones in tissue-specific gene expression. Therefore, the ultimate basis for our research is to determine whether histone modifications directly correlate with DNA methylation in regulating differential gene expression.