Abstract
Genomic imprinting is an iconic epigenetic phenomenon in which genes are expressed from one allele only, in a parent-specific manner. Within vertebrates, genomic imprinting is only found in live-bearing mammals, and is regulated by sex-specific DNA methylation marks established during primordial germ cell development which are then passed on to the next generation. While the parental conflict hypothesis offers some insight, it is largely unknown why genomic imprinting was selected for in the ancestors of marsupial and eutherian mammals – a lack of studies outside of human/murine models hampers this understanding. To address this, I searched for novel imprinted genes in the rabbit and cattle. My experimental approach centred on whole genome long-read nanopore sequencing, a technique recently shown to be useful in detecting allele-specific methylation associated with imprinting.
I first focussed on MLH1, the driver of human Lynch syndrome which involves predisposition to a spectrum of cancers, as recently it was been shown to be imprinted in marsupials. Lynch syndrome is often caused by constitutional epimutations, which are similar in some respects to imprinting, implying a link between MLH1 pathology and imprinted gene evolution. However, my work showed that neither rabbit nor cattle possess differential methylation of MLH1, thus provided limited support for this hypothesis.
Following this, I expanded my search for novel imprinted gene candidates by identifying allele-specific DNA methylation genome-wide. My analysis revealed 22 genes known to be imprinted in mammals, such as IGF2R and PEG10, as well as 24 novel candidates, including DLL3, a key gene in the notch pathway, HOXD3, a critical gene involved in limb and genital development, BOP1, a regulator of the cell cycle, and FANCC, a gene involved Fanconi anaemia pathway that has been predicted to be imprinted. Further evidence was provided for these candidates by exploring CpG island associations, adjacent genes, and gene function. Future research should focus on examining the expression of these candidates and the parent-sex of the expressed allele to definitively determine their imprinting status.