IPW (imprinted gene in the Prader-Willi syndrome region), a long non-coding RNA, is a paternally expressed gene in the PWS/AS imprinted domain on human chromosome 15 and mouse chromosome 7. Disruption of the PWS/AS region is associated with three neurogenic disorders in humans. In this study, we identified the bovine homolog of the IPW gene; multiple transcripts obtained by RT-PCR and RACE showed a complex and tissuespecific expression pattern of IPW in the brain, heart, kidney, liver, lung, spleen and skeletal muscle. An informative single nucleotide polymorphism (rs133341090) in the long exon H was identified by sequencing the genomic DNA, and mono-allelic expression of IPW was confirmed by sequencing the cDNAs of heterozygous individuals, indicating that IPW may be imprinted in cattle. The protein-coding potential of IPW transcripts was assessed using CODING POTENTIAL CALCULATOR (CPC) software, which showed a negative score. In addition, sequencing analysis also indicated multiple small open reading frames in the bovine IPW transcript, but none of the ATGs was consistent with Kozak consensus. Taken together, the IPW transcripts are most likely long non-coding RNAs.

SummaryGenomic imprinting is a rare epigenetic process in mammalian cells that leads to monoallelic expression of a gene with a parent‐specific pattern. The UBE3A (ubiquitin protein ligase E3A) gene is imprinted with maternal allelic expression in the brain but biallelically expressed in all other tissues in humans. The silencing of the paternal UBE3A allele is thought to be caused by the paternally expressed antisense RNA transcript of UBE3A‐ATS. The aberrant imprinted expression of the UBE3A is associated with several neurodevelopmental syndromes and psychological disorders. Cattle are a valuable model species in determining the genetic etiology of sporadic human disorder, and maternal expression of UEB3A has been revealed by next‐generation sequencing study in the bovine conceptus. In this study, we investigated the allelic expression of UBE3A and UBE3A‐ATS in adult bovine somatic tissues. To confirm the splicing pattern of bovine UBE3A, five 5′ alternative transcripts (MT210534–MT210538) were first obtained from bovine brain tissue by RT‐PCR. Based on 10 SNP genotypes, we found that the brain‐specific monoallelic expression of bovine UBE3A did not occur along the entire locus, and there was a shift from biallelic expression to monoallelic expression in exon 14 of the UBE3A gene. However, the brain‐specific monoallelic expression of bovine UBE3A‐ATS occurred in the entire gene. These observations demonstrated that the monoallelic expression did not occur along the bovine UBE3A entire locus and was associated with the genomic position.