The International Swine Methylome Consortium (ISMC): Supporting epigenomics and biomedical research

K. Schachtschneider, L. Rund, O. Madsen, R. Johnson, A. Archibald, C. Park, M. Groenen, L. Schook
Swine in Biomedical Research Meeting, July 6-8, 2014, Raleigh, NC


Pigs (Sus scrofa) are an important biomedical model due to their anatomical, behavioural, genetic and physiological similarities with humans, as well as their availability, short generation interval and large litter size. Studies using pigs have been shown to be more predictive of therapeutic treatments in humans than rodent studies, and are currently being used to study a variety of human diseases including Huntington's, Alzheimer's and cardiovascular diseases. DNA methylation is an epigenetic mark that occurs at cytosines throughout the genome, and altered methylation levels are associated with aberrant gene transcription. Furthermore, DNA methylation represents a link between genetics and environmental signals that has been reported to play an important role in human pathologies including cancer and neurological disorders, revealing the importance of accessing DNA methylation patterns in understanding disease development. The International Swine Methylome Consortium (ISMC) was created to produce a porcine methylome map in order to enhance studies of DNA methylation patterns and their association with the development and detection of relevant human diseases. Reduced representation bisulfite sequencing and RNAseq libraries are being used to target CpG islands and assess gene transcription for biomedically relevant tissues and developmental time points. In a preliminary exploratory study, eight tissue samples (from the adult female Duroc utilized for the pig genome sequencing project) were analysed. Additional samples identified for development of the swine methylome map will consist of biomedically relevant tissue samples from Yucatan, Sinclair, Minnesota and NIH mini-pig breeds, as well as commercial domestic breeds. Breeds were chosen based on their availability and use by biomedical researchers. The tissue types and developmental time points were prioritized to ensure a high quality methylome map of broad utility for the biomedical community. These resources will facilitate future biomedical research in pigs, ensuring they remain an important human disease model.

Funding: Jeju National University of Rural Development Administration of the Republic of Korea (538 JNU Korea 2012-06052)