Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses

Abstract

Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date, 263 imprinted genes have been identified among all investigated mammalian species. However, only 21 have been described in sheep, of which 11 are annotated in the current ovine genome. Here, we aim to i) use DNA/RNA high throughput sequencing to identify new monoallelically expressed and imprinted genes in day 135 ovine fetuses and ii) determine whether maternal diet (100%, 60%, or 140% of National Research Council Total Digestible Nutrients) influences expression of imprinted genes. We also reported strategies to solve technical challenges in the data analysis pipeline. We identified 80 monoallelically expressed, 13 new putative imprinted genes, and five known imprinted genes in sheep using the 263 genes stated above as a guide. Sanger sequencing confirmed allelic expression of seven genes, CASD1, COPG2, DIRAS3, INPP5F, PLAGL1, PPP1R9A, and SLC22A18. Among the 13 putative imprinted genes, five were localized in the known sheep imprinting domains of MEST on chromosome 4, DLK1/GTL2 on chromosome 18 and KCNQ1 on chromosome 21, and three were in a novel sheep imprinted cluster on chromosome 4, known in other species as PEG10/SGCE. The expression of DIRAS3, IGF2, PHLDA2, and SLC22A18 was altered by maternal diet, albeit without allelic expression reversal. Together, our results expanded the list of sheep imprinted genes to 34 and demonstrated that while the expression levels of four imprinted genes were changed by maternal diet, the allelic expression patterns were un-changed for all imprinted genes studied.

The Landscape of Genomic Imprinting at the Porcine SGCE/PEG10 Locus from Methylome and Transcriptome of Parthenogenetic Embryos

“…In general, expression patterns in the porcine embryos within the syntenic region were closer to the expression in humans than that of mice, but in the pig the PPP1R9A gene showed biallelic expression in all tested tissues [embryonic and 2-day-old in the current study, and 2-month-old as reported in (Zhang et al 2011)]. This biallelic expression of porcine PPP1R9A was different from the mouse and human which showed maternal expression in embryonic or fetal skeletal muscle tissues (Nakabayashi et al 2004;Monk et al 2008) and ovine fetuses that showed maternal expression in the kidney (Duan et al 2018). Our polymorphism-based analysis revealed biallelic expression of PPP1R9A in the muscle and kidney in 2-day-old neonates (Figure 4).…”

“…Another study revealed that expression of PPP1R9A is biallelic in multiple tissues of 2-month-old piglets, except skeletal muscle, fat, and testis in which expression of PPP1R9A was not detectable (Zhang et al 2011). To confirm whether or not allele-specific expression of PPP1R9A occurs in neonatal pigs, polymorphism-based assays were conducted for both parents and offspring and it revealed a biallelic expression of PPP1R9A which is different from its maternal expression in the mouse, human, and sheep (Ono et al 2003;Nakabayashi et al 2004;Duan et al 2018).…”

“…The telomeric (distal) boundary of the large imprinted cluster organized around Sgce/Peg10 locus in the mouse proximal region toward the centromere of chromosome 6 (6A1) reaches the Asb4 gene, based on previous reports on maternally expression of Ppp1r9a, Pon3, Pon2, and Asb4 in mice (Piras et al 2000;Mizuno et al 2002;Ono et al 2003;Nakabayashi et al 2004). However, the boundary spans between CASD1 and PON3 in sheep (Duan et al 2018), while in the human it spans between SGCE and PPP1R9A (Ono et al 2001;Grabowski et al 2003;Okita et al 2003;Monk et al 2008). In addition, there are reports about monoallelic expression of mouse Calcr and Tfpi2 and human CALCR (in brain) and TFPI2 toward the centromeric (proximal) region, but the expression of those genes was restricted to brain and placenta, respectively (Hoshiya et al 2003;Monk et al 2008).…”

“…Human PPP1R9A gene was found to be imprinted and maternally expressed mainly in skeletal muscle tissues (Nakabayashi et al 2004). In ovine fetuses, a putative imprinted interval was reported to be extended to between CASD1 (maternally expressed) and PON3 (paternally expressed), while the paternal expression of SGCE and PEG10 and maternal expression of PPP1R9A were conserved (Duan et al 2018).…”

Exploring the Role of Maternal Nutritional Epigenetics in Congenital Heart Disease

“…This underlines the influence of critical environmental factors during pregnancy, and maternal nutrition is one such factor ( 44 ). Inadequate maternal nutrition during pregnancy was proven to alter the DNA methylation pattern and expression of certain imprinted genes such as Insulin Like Growth Factor 2 Receptor ( IGF2R ) and H19 Imprinted Maternally Expressed Transcript ( H19 ) in ovine fetuses ( 45 ).…”