ZFAT (isoform-specific) and its antisense RNA 1 (ZFAT-AS1) are two allele-specific monoallelically expressed genes in cattle.

In mammals, imprinted genes are characterised by a monoallelic expression, which is based on parental origin and is essential for both foetal and placental development. The ZFAT gene encodes a transcriptional factor, and its non-coding antisense RNA, ZFAT-AS1, overlaps with the ZFAT locus. Both ZFAT and ZFAT-AS1 are maternally imprinted in human placentas. In bovines, the imprinting status of the ZFAT and ZFAT-AS1 genes has yet to be reported. In this study, we analysed the allelic expression of three transcript variants (X1-X3) of the bovine ZFAT and ZFAT-AS1 genes in somatic tissues and placentas using a single nucleotide polymorphism-based method. The results showed that bovine ZFAT exhibited isoform-specific paternal expression. The ZFAT X2 variant exhibited monoallelic expression in the bovine placentas and biallelic expression in the six bovine somatic tissues (heart, liver, spleen, lung, kidney and brain). However, the ZFAT X1 and X3 variants were biallelically expressed in both bovine tissues and placentas. A 311 bp bovine ZFAT-AS1 complementary DNA (cDNA) sequence was obtained by aligning the human ZFAT-AS1 cDNA sequence with the bovine genome and conducting reverse transcription polymerase chain reaction amplification. Bovine ZFAT-AS1 have monoallelic expression in bovine placentas and somatic tissues. In addition, the DNA methylation of two regions was characterised, including the partial promoter, and exon 1 and intron 1 regions of ZFAT, and there were no differentially methylated regions.