Detecting imprinted genes in the pig genome by high-throughput cDNA-sequencing (RNA-seq)

O. Madsen, R.P.M.A. Crooijmans, L.A. Rund, L.B. Schook, M.A.M. Groenen
Plant and Animal Genome XVIII Conference, January 10-14, 2010, San Diego, CA


Genomic imprinting is an epigenetic phenomenon, where the level of expression of alleles depends on their parental origin. In mammals around 100 genes have experimentally been shown to be imprinted, mainly by studies in human and mouse. Studies in other mammals for imprinted genes are relative sparse and some of the imprinted genes have been shown to be species-specific imprinted. This suggests that in mammals the evolution of genomic imprinting, is a dynamic and ongoing process. A systematic investigation of imprinted genes in other mammals therefore is essential to achieve a detailed understanding of the evolution of imprinted genes in relation to their key role in brain development and regulation of growth and reproduction.

High-throughput DNA sequencing of transcriptomes (RNA-seq) is a powerful new tool for e.g. detecting alternative splicing; quantifying gene expression levels and distinguish allele specific expression. The latter makes RNA-seq a very valuable method for validating known and detecting novel imprinted genes. This study aims to detect both established and novel imprinted genes in the placenta of pigs. cDNA from placenta of a clone of the sequenced pig “Tabasco” has been paired-end sequenced by the Illumina GA2 technology. These RNA-seq sequences will be compared against known Tabasco specific SNPs to detect mono-allelic expression. Results from these analyses will be presented.

Research also presented at Society for Molecular Biology and Evolution Annual Meeting, July 4-8, Lyon, France.