Figure 1.
Differentially expressed genes in maternal undernutrition model.
(A) Venn's diagrams showing the number of differentially expressed gene probes in comparisons MLP vs. C (P-C), MLP-F vs. C (F-C) and MLP vs. MLP-F (P-F) at FDR 5% (top) and FDR 1% (bottom). Number of gene probes whose expression was unaltered is indicated in black (right). Numbers of altered gene probes in MLP-C contrast at different FDR are indicated in green (left). (B) qRT-PCR mRNA analysis for 8 genes: Dnmt1, Dnmt3a, Dnmt3b, Aurkb, Mcm6, Hat1, Gnmt and Gmnn. Results are given in relative units, as ratio of number of copies in assessed gene and housekeeping gene GAPDH. × P<0.05; ×× P<0.01; ××× P<0.001. ns P>0.05.
Figure 2.
Figure panel representing five genomic loci (Agtrap, Fgf5, Dnmt1, Mcm6, Sfmbt1) containing differentially methylated regions (DMRs) between livers obtained from newborns whose mothers were fed a control diet (18% protein) and livers obtained from newborns whose mothers were fed a low protein (9% protein) diet.
For each locus, Panel A shows the validation data obtained from bisulfite conversion followed by cloning and sequencing, which provides methylation status at single CpG site resolution for different livers and different clones (black circles represent methylated CpG, white circles unmethylated CpG). All loci except for Sfmbt1 validated significant difference in DNA Methylation (Agtrap P<0.01, Fgf5 P<0.01; Dnmt1 P<0.05; Mcm6 P<0.01, Mann-Whitney U test), in line with that indicated by genome-wide MBD-Seq data. Panel B provides an overview of the genomic locus, the gene structure, the location of the DMR validated, and the level of methylation across the locus for each of the animal groups analyzed (Control = “cmbd”, Low Protein = “pmbd”, and Low Protein with Folic Acid Supplementation = “fmbd”). Panel C summarises the percent methylation in control and low protein for each locus assessed by bisulphite sequencing.
Table 1.
List of loci from selected GWAS studies pertaining to metabolic and cardiovascular phenotypes associated to Low Protein diet that contain differentially methylated regions in their orthologous rat locus.
Figure 3.
Intersection of differentially expressed (GEX), separated in up-regulated (UP) and down-regulated (DW), and DMRs-neighboring (MBD) genes.
At FDR 5% only 15 genes (hypergeometric probability = 0.69) are found in both lists, of which 6 were down-regulated (Dym, Glrx2, Mlph, Myh10, Pftk1, And Prep) and 9 up-regulated (Abcc8, Abhd6, Cep350, Ctsa, Eif2b3, Pdk1, Serpina11, Tpcn2, And Tyw3). The total number of mapped genes is 555 in MBD and 577 in GEX.