Detection of porcine imprinted genes through high-throughput cDNA-sequencing (RNA-seq)

O. Madsen, D. Radjabzadeh, R. Crooijmans, L.A. Rund, L.B. Schook, M. Groenen
13th Congress of the European Society for Evolutionary Biology, August 19-24, 2011, Tubingen, Germany


Genomic imprinting is an epigenetic phenomenon in which the levels of allelic expression are dependent upon parental origin.  In mammals >100 genes have been shown to be imprinted, mainly through studies in humans and mice. Studies in other mammals for imprinted genes are relatively sparse and have generally been limited to either an ad hoc single gene analysis or analyses on "unnatural" systems such as uniparental embryos. While some genes are imprinted in all tissues throughout all stages of development others are imprinted in e.g. a particular stage of development. Imprinted genes play important roles in many stages of development, and dysregulation of imprinted genes can result in diseases such as cancer and neurological disorders. Since the pig is one of the most widely used model organism for human diseases and biomedical research, a comprehensive investigation of imprinted genes in pigs contributes to a detailed understanding of the evolution of imprinted genes in relation to their key role in brain development, regulation of growth and reproduction.

RNA-seq is a powerful tool to analyze allele specific expression and therefore provides an excellent opportunity for detecting imprinted genes, by comparing the genetic variation present in a genome with the variation in allelic expression. By combining this information with the variation present in the genome of the parents, it will be possible to detect imprinted genes.

This study aims to detect the whole range of imprinted genes (the imprintome) in pigs. This will be done by whole genome sequencing of two family trios (father, mother and offspring) plus RNA-seq of tissues from the two offspring (starting out with placenta, brain and liver). Results from these analyses will be presented and related to the imprintome of other eutherian mammals.

Research also presented at the 7th International Symposium on Integrative Bioinformatics, March 21-23, Wageningen, The Netherlands.