Workshop Report 30

Practical experience with rodent species used in toxicology studies: what is a normal epigenetic background?

Richard Meehan
Group Leader, Chromosome Biology,
MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
Modification of DNA resulting in 5-methylcytosine (5-mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. MRC has developed a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; “DIP-SC-seq”) on the Ion Proton sequencer. Focusing on the 5hmC and 5mC marks we can demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than four days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets. The MRC wishes to apply this method to characterise the ‘ground state’ of liver epigenomes from commonly utilised rodent models. Dr Meehan presented his group’s initial analysis of male and female 5hmC epigenomes from Wistar and SD rat liver. There was essentially little variation within strain samples but appreciable differences between strains. Gender specific differences can also be detected that are linked to expression patterns. This information will be useful in planning future experimental strategies.
Epigenetic perturbations have been associated with exposure to a range of drugs and toxicants, including non-genotoxic carcinogens (NGCs). Although a variety of epigenetic modifications induced by NGCs have been studied previously, the MRC’s recent genome-wide integrated epigenomic and transcriptomic studies using targeted array platforms, revealed for the first time the extent and dynamic nature of the epigenetic perturbations resulting from xenobiotic exposure. The interrogation and integration of genome wide 5hmC modification states, with other epigenetic modification and expression profiling studies, has the potential to identify unique epigenetic signatures for diverse drug exposure studies. These studies and methodologies can enhance mechanistic understanding of xenobiotic exposure and provide for the identification of novel safety biomarkers that will be of benefit in multiple clinical and safety studies.