Investigation of genomic imprinting in cattle

Genomic imprinting is an epigenetic mechanism whereby a subset of genes, called imprinted genes, show parent-of-origin-dependent monoallelic expression. Most imprinted genes are regulated by allele-specific DNA methylation at differentially methylated regions (DMRs). Although major imprinted genes and DMRs have already been identified in human and mouse, information on genomic imprinting is sporadic and limited in other mammalian species due to the cost and technical difficulties of genome-wide allele-specific gene expression and DNA methylation analyses. Here we propose two strategies to predict DMRs from whole-genome bisulfite sequencing (WGBS) data: one is based on conservation and the other is on germline DNA methylation patterns. Both strategies do not require genotype information and predict DMRs with high sensitivity and low background. We applied these strategies to human, rhesus, mouse and cow and estimated the evolutionary trajectory of individual DMRs. These analyses suggest that various factors, including CpG density, germline methylation and sequence-specific DNA binding proteins, may contribute to species-specific differences in genomic imprinting. Our strategies will facilitate cross-species comparison of genomic imprinting and identification of novel DMRs. Overall design: Genomic DNA was purified with phenol/chloroform extraction and ethanol precipitation. WGBS libraries were constructed using the post-bisulfite adapter-tagging (PBAT) method. The PBAT libraries were sequenced on the HiSeq 2500 platform (Illumina, CA, USA) with 101-bp single-end reads.