Prediction accuracy of alternative strategies.

<p>Prediction accuracy of alternative strategies.</p

Accuracy of KNN* using different evaluation methods.

<p>Accuracy of KNN* using different evaluation methods.</p

Prediction accuracy on randomly chosen genes.

<p>(a) Gene-profile accuracy as a function of . (b) Gene-profile accuracy for each time point.</p

Significant Species-Specific Motifs Discovered in the Putative Promoters of MicroRNA Genes in Four Species.

<p>(A–C) The same as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030037#pcbi-0030037-g002" target="_blank">Figure 2</a>.</p

Significant Conserved Motifs Discovered in the Putative Promoters of the Four Species

<div><p>(A) The number of microRNA genes that contain the corresponding motifs in their upstream.</p><p>(B) Expected frequencies of the corresponding motifs.</p><p>(C) <i>Z</i>-scores obtained by Monte Carlo Simulations (see the section Motif Analysis).</p></div

The Distribution of the Distances between Putative Promoters and MicroRNA Hairpins

<p>The horizontal axis shows the positions of putative promoters with respect to the corresponding microRNA hairpins and the vertical axis shows the percentage of microRNA genes that have putative promoters at the specified positions.</p

The Distributions of CT Repeats

<p>The first group to the left of the figure shows the distributions of CT repeats in the genomes of the four species studied, estimated by a Monte Carlo simulation. The subsequent groups show the distributions of CT repeats in the upstream of microRNA hairpins. The vertical axis is the percentage of microRNA genes and randomly sampled sequences that contain CT repeats (see text).</p

Alterations in the placental methylome with maternal obesity and evidence for metabolic regulation

<div><p>The inflammatory and metabolic derangements of obesity in pregnant women generate an adverse intrauterine environment, increase pregnancy complications and adverse fetal outcomes and program the fetus for obesity and metabolic syndrome in later life. We hypothesized that epigenetic modifications in placenta including altered DNA methylation/hydroxymethylation may mediate these effects. Term placental villous tissue was collected following cesarean section from lean (prepregnancy BMI<25) or obese (BMI>30) women. Genomic DNA was isolated, methylated and hydroxymethylated DNA immunoprecipitated and hybridized to the NimbleGen 2.1M human DNA methylation array. Intermediate metabolites in placental tissues were measured by HPLC-ESI-MS, ascorbate levels by reverse phase HPLC and gene expression by RT-PCR. Differentially methylated and hydroxymethylated regions occurred across the genome, with a 21% increase in methylated but a 31% decrease in hydroxymethylated regions in obese vs lean groups. Whereas increased methylation and decreased methylation was evident around transcription start sites of multiple genes in the <i>GH/CSH</i> and <i>PSG</i> gene clusters on chromosomes 17 and 19 in other areas there was no relationship. Increased methylation was associated with decreased expression only for some genes in these clusters. Biological pathway analysis revealed the 262 genes which showed reciprocal differential methylation/ hydroxymethylation were enriched for pregnancy, immune response and cell adhesion-linked processes. We found a negative relationship for maternal BMI but a positive relationship for ascorbate with α-ketoglutarate a metabolite that regulates ten eleven translocase (TET) which mediates DNA methylation. We provide evidence for the obese maternal metabolic milieu being linked to an altered DNA methylome that may affect placental gene expression in relation to adverse outcomes.</p></div

Relationship between maternal adiposity, intermediary metabolites and placenta-specific gene expression.

<p>(A-C) Correlations between placental levels of αKG and maternal BMI (A) or ascorbate (B), and between αKG and <i>CSHL1</i> mRNA levels (C). The relations between continuous variables were evaluated by Spearman correlations (*<i>P</i> < 0.05). Pre-pregnancy or first trimester BMI was used as maternal early BMI.</p

Widespread alterations to the placental epigenome identified throughout the genome in the setting of maternal obesity.

<p>(A) Chromosome ideograms showing the genome-wide distributions of methylated and hydroxymethylated peak regions. Differences in 5mC and 5hmC distributions between placentas of obese vs. lean pregnancies (n = 10 placentas combined each group) were found widespread across the genome. Red and blue vertical lines indicate locations of methylated and hydroxymethylated genomic regions, respectively. Adjacent upper and lower lines represent peak regions detected in lean and obese pregnancies, respectively. The locations of the <i>GH-CSH</i> gene cluster on chromosome 17q24 and <i>PSG</i> gene cluster on chromosome 19q13 are indicated by closed circles. The pregnancy-associated miRNA cluster is also located on chromosome 19q13 (closed triangle). (B) Number of methylated (5mC) and hydroxymethylated (5hmC) peak regions identified by MeDIP and hMeDIP assays. Increased numbers of methylated peaks (right panel) and decreased numbers of hydroxymethylated peaks (left panel) were consistently detected at various parts of the genome including CpG islands, CpG island shores and shelves.</p