Maternal dietary methionine restriction alters hepatic expression of one-carbon metabolism and epigenetic mechanism genes in the ducklings

Abstract

Background: Embryonic and fetal development is very susceptible to the availability of nutrients that can interfere with the setting of epigenomes, thus modifying the main metabolic pathways and impacting the health and phenotypes of the future individual. We have previously reported that a 38% reduction of the methyl donor methionine in the diet of 30 female ducks reduced the body weight of their 180 mule ducklings compared to that of 190 ducklings from 30 control females. The maternal methionine-restricted diet also altered plasmatic parameters in 30 of their ducklings when compared to that of 30 ducklings from the control group. Thus, their plasma glucose and triglyceride concentrations were higher while their free fatty acid level and alanine transaminase activity were decreased. Moreover, the hepatic transcript level of 16 genes involved in pathways related to energy metabolism was significantly different between the two groups of ducklings. In the present work, we continued studying the liver of these newly hatched ducklings to explore the impact of the maternal dietary methionine restriction on the hepatic transcript level of 70 genes mostly involved in one-carbon metabolism and epigenetic mechanisms.

Results: Among the 12 genes (SHMT1, GART, ATIC, FTCD, MSRA, CBS, CTH, AHCYL1, HSBP1, DNMT3, HDAC9 and EZH2) identified as differentially expressed between the two maternal diet groups (p-value < 0.05), 3 of them were involved in epigenetic mechanisms. Ten other studied genes (MTR, GLRX, MTHFR, AHCY, ADK, PRDM2, EEF1A1, ESR1, PLAGL1, and WNT11) tended to be differently expressed (0.05 < p-value < 0.10). Moreover, the maternal dietary methionine restriction altered the number and nature of correlations between expression levels of differential genes for one-carbon metabolism and epigenetic mechanisms, expression levels of differential genes for energy metabolism, and phenotypic traits of ducklings.

Conclusion: This avian model showed that the maternal dietary methionine restriction impacted both the mRNA abundance of 22 genes involved in one-carbon metabolism or epigenetic mechanisms and the mRNA abundance of 16 genes involved in energy metabolism in the liver of the newly hatched offspring, in line with the previously observed changes in their phenotypic traits.

Keywords: Avian; Differentially expressed genes; Duck; Methyl donor; Nutritional programming.

Fig. 1

Exploratory data analyses. A Score plot of a PLS performed on the data of the 62 studied genes: The ducklings from R group and C group are represented with triangles and circles, respectively. The females are in red and the males in blue. The two latent variables summarized respectively 28% (horizontal axis) and 10% (vertical axis) of the whole variability. B Biplot of a PCA performed on the data of the 22 differential genes: The male ducklings from the R group (MR) and the C group (MC) are represented in red crosses and grey squares, respectively, and the females from the R group (FR) and the C group (FC) are in yellow triangles and blue circles, respectively. The first principal component (horizontal axis) explained 43.1% of the whole variability and discriminated the samples according to the diet received by the dams (R groups on the left side versus C groups on the right side). The second principal component (vertical axis) explained 10.2% of the whole variability and slightly discriminated the two sexes in the C group only. In addition, the correlation circles showed correlations between the 22 differential genes and the two main principal components and show an opposite regulation pattern of GLRX and MTR when compared to the 20 other differential genes. For both Fig. 1A and B, the qqnorm transformed normalized relative expressions were used

Fig. 2

Correlation matrices between the gene expression of the 22 differential genes and the phenotypic traits of the ducklings. The correlation matrices were plotted for the R group (n = 18), the C group (n = 17), and the males (n = 19) and the female ducklings (n = 16) separately. The phenotypic traits are body weight, liver weight, percentages of liver lipids (Lipid) and liver dry mater (DM), plasma activities of ALP, ALT and AST and plasma concentrations of triglycerides (Triglycerid) and free fatty acids (FFA). The color scale indicates the strength of the correlation; blue for a positive correlation and red for a negative one. Only the significant correlations (with a P-value < 0.05) were plotted. For the genes, the imputed but not qqnorm transformed, normalized relative expressions were used and for the phenotypic data the raw values were used

Fig. 3

Correlation matrices between the gene expression of the two subsets of genes. The correlation matrices were plotted for the R group (n = 18) and the C group (n = 17). The group of differential genes involved in energy metabolism is referred as “Subset 1” and the group of differential genes identified in this study and mostly involved in one carbon metabolism and epigenetic mechanisms is referred as “Subset 2”. The color scale indicates the strength of the correlation; blue for a positive correlation and red for a negative one. Only the significant correlations (with a P-value < 0.05) were plotted. The square represents the correlations between the 16 DEGs of energy metabolism and the 22 differential genes of the one-carbon metabolism and epigenetic mechanisms. The imputed but not qqnorm transformed, normalized relative expressions were used

Fig. 4

Role of the 22 differential genes assigned to one-carbon metabolism and epigenetic mechanisms and their regulation in newly hatched ducklings from the R group (adapted from Clare et al. [15],). Only the genes that have been studied in this work are mentioned. The folate cycle is represented in green and the methionine cycle is represented in blue. The differential genes for the maternal diet that are downregulated or upregulated when comparing the R group ducklings to the C group ducklings are in blue and red, respectively. The 12 DEGs (with a Diet p-value (BH) <  0.05) are in bold whereas the 10 ones which tend to be differently expressed between the two diet groups (with a Diet p-value (BH) <  0.10) are not. They were all downregulated in the R group samples when compared to C group samples, except GLRX and MTR that were upregulated. ADK, Adenosine Kinase; AHCY, Adenosylhomocysteinase; AHCYL1, Adenosylhomocysteinase Like 1; ATIC, 5-Aminoimidazole-4-Carboxamide Ribonucleotide Formyltransferase/IMP Cyclohydrolase; BHMT/2, Betaine--Homocysteine S-Methyltransferase/2; CBS, Cystathionine Beta-Synthase; CHDH, Choline Dehydrogenase; CTH, Cystathionine Gamma-Lyase; DHFR, Dihydrofolate Reductase; DNMT3A, DNA Methyltransferase 3 Alpha; EZH2, Enhancer Of Zeste 2 Polycomb Repressive Complex 2 Subunit; FTCD, Formimidoyltransferase Cyclodeaminase; GART, Phosphoribosylglycinamide Formyltransferase; GLRX, Glutaredoxin; MAT2B, Methionine denosyltransferase 2B; MSRA, Methionine Sulfoxide Reductase A; MTHFD1/2, Methylenetetrahydrofolate Dehydrogenase1/2; MTHFD1L, Methylenetetrahydrofolate Dehydrogenase (NADP+ Dependent) 1 Like; MTHFR, Methylenetetrahydrofolate Reductase; MTR, 5-Methyltetrahydrofolate-Homocysteine Methyltransferase; MTRR, 5-Methyltetrahydrofolate-Homocysteine Methyltransferase Reductase; PLAGL1, PLAG1 Like Zinc Finger 1; PRDM2, PR/SET Domain 2; SHMT1, Serine Hydroxymethyltransferase 1; TYMS, Thymidylate Synthetase; WNT11, Wnt family member 11. DHF, dihydrofolate; dTMP, thymidine monophosphate; dUMP, deoxyuridine monophosphate; HCY, homocysteine; MET, methionine; SAH, S-adenosylhomocysteine; SAM, S-adenosylmethionine; THF, tetrahydrofolate. HDAC9, Histone Deacetylase 9; EEF1A1, Eukaryotic translation elongation factor 1 alpha 1; HSBP1, Heat Shock factor binding protein 1; ESR1, estrogen receptor 1