Journal: PLoS ONE

Article Title: Early Life Stress Inhibits Expression of Ribosomal RNA in the Developing Hippocampus

doi: 10.1371/journal.pone.0115283

Figure Lengend Snippet: A. rRNA levels peak during the second week of life. B. (top), a representative pyrogram of the pyrosequencing assay used to assess DNA methylation (blue) lines, (bottom) schematic diagram of the rDNA promoter elements. C. DNA methylation at the rDNA is lower in PND14 compared to PND7 and PND63 for CG_3 and CG_6. D. DNA methylation levels at CG_6 on PND7, 14, and 63. One-way ANOVA followed by Tukey-post hoc analysis when compared to PND14 (A, D), repeated measures ANOVA followed by simple-effect analysis (C). Error bars represent mean ± SEM, *p<0.05. UCE-upstream core element, To- Proximal-promoter terminator sequence.

Article Snippet: Three hundred nanograms of genomic DNA were bisulfite treated with the EZ DNA Methylation-Gold Kit (Zymo Research, Cat# D 5005) according to manufacturer instruction.

Techniques: Pyrosequencing Assay, DNA Methylation Assay, Sequencing

Journal: PLoS ONE

Article Title: Early Life Stress Inhibits Expression of Ribosomal RNA in the Developing Hippocampus

doi: 10.1371/journal.pone.0115283

Figure Lengend Snippet: Exposure to BDS decreases total amount of DNA (A) and RNA (B) harvested from the hippocampus of 14-day old pups. C. Relative levels of rRNA are lower in BDS compared to control 14-d old pups. Exposure to BDS increases DNA methylation at CG_6 (D and E). Unpaired Student t tests (A, B, C, E), Repeated measures ANOVA followed by simple-effect analysis (D). Error bars represent mean ± SEM, *p<0.05.

Article Snippet: Three hundred nanograms of genomic DNA were bisulfite treated with the EZ DNA Methylation-Gold Kit (Zymo Research, Cat# D 5005) according to manufacturer instruction.

Techniques: DNA Methylation Assay

Journal: PLoS ONE

Article Title: Early Life Stress Inhibits Expression of Ribosomal RNA in the Developing Hippocampus

doi: 10.1371/journal.pone.0115283

Figure Lengend Snippet: A (top) Nucleotide sequence of primer rRNA-2F (arrow) is shown with HpaII restriction site at CG_6 is highlighted in grey, (bottom), schematic diagram of Q-PCR primers used to assess DNA methylation at CG_6. Note that no product will be generated if CG_6 is not methylated and the DNA is digested with HpaII. Exposure to BDS decreases rRNA levels (B) while increasing DNA methylation at CG_6 in 14-day old pups (C). D. Levels of methylation at CG_6 are inversely correlated with rRNA levels in the developing hippocampus. Unpaired Student t tests (B, C), Pearson correlation (D). Error bars represent mean ± SEM, *p<0.05.

Article Snippet: Three hundred nanograms of genomic DNA were bisulfite treated with the EZ DNA Methylation-Gold Kit (Zymo Research, Cat# D 5005) according to manufacturer instruction.

Techniques: Sequencing, DNA Methylation Assay, Generated, Methylation

Journal: PLoS ONE

Article Title: Early Life Stress Inhibits Expression of Ribosomal RNA in the Developing Hippocampus

doi: 10.1371/journal.pone.0115283

Figure Lengend Snippet: Exposure to BDS decreases total amount of DNA (A), but not RNA (B), harvested from the hippocampus of 28-day old offspring. C. Relative levels of rRNA are similar in BDS compared to control 28-d old mice. The effects of BDS on DNA methylation at CG_6 do not persist in 28-day old mice (D and E). Unpaired Student t tests (A, B, C, E), Repeated measures ANOVA (D). Error bars represent mean ± SEM, *p<0.05.

Article Snippet: Three hundred nanograms of genomic DNA were bisulfite treated with the EZ DNA Methylation-Gold Kit (Zymo Research, Cat# D 5005) according to manufacturer instruction.

Techniques: DNA Methylation Assay

Journal: PLoS ONE

Article Title: Early Life Stress Inhibits Expression of Ribosomal RNA in the Developing Hippocampus

doi: 10.1371/journal.pone.0115283

Figure Lengend Snippet: Three hours of maternal separation in 14-day old pups increased plasma levels of corticosterone (A), reduced rRNA levels in the hippocampus (B), and increased DNA methylation at the rDNA promoter (C), most notably CG_6 site (D). Unpaired Student t tests (A, B, D), Repeated measures ANOVA followed by simple-effect analysis (C). Error bars represent mean ± SEM, *p<0.05, **p<0.01.

Article Snippet: Three hundred nanograms of genomic DNA were bisulfite treated with the EZ DNA Methylation-Gold Kit (Zymo Research, Cat# D 5005) according to manufacturer instruction.

Techniques: DNA Methylation Assay

Journal: Current environmental health reports

Article Title: Adverse Maternal Metabolic Intrauterine Environment and Placental Epigenetics: Implications for Fetal Metabolic Programming

doi: 10.1007/s40572-018-0217-9

Figure Lengend Snippet: Global DNA methylation and epigenome-wide studies of gestational diabetes, maternal glucose and obesity

Article Snippet: Cardenas et al 2018 Ref. 65 , N= 448 French-Canadian Canada Gen3G Birth Cohort Sherbrooke, Quebec , Maternal glucose following 2h post-OGTT test (2nd trimester, wk 24–28) , 850K Infinium Methylation BeadChip EPIC Array Bisulfite DNA Pyrosequencing , Robust linear regression models adjusted for maternal age, BMI, parity, smoking during pregnancy, gestational age, sex and the first 10 principal components estimated from a reference-free cell-type heterogeneity method as proxy for cellular heterogeneity. P-values adjusted with FDR at 5% (q-value<0.05) Bisulfite DNA pyrosequencing for replication in another smaller population (N=65 to 108). , Seven CpG sites (q<0.05) associated with ↑ 1 mMol/L 2h-glucose postOGTT: TNFRSF1B (cg26189983) 1.22% ↑ methylation PDE4B (cg07734160, cg13866577, cg03442467, cg13349623) ↓ methylation (−0.58 to −1.16%) BLM (cg20254265) −0.63% ↓ methylation LDLR (cg08483713) −0.27% ↓ methylation. PDE4B methylation (cg03442467 gene body/TSS200) correlated with PDE4B ↑ expression (r=0.31; P=1.81×10 −3 ), TNFRSF1B methylation (cg26189983) correlated with expression (r= −0.24; P=0.013). LDLR methylation (cg08483713 gene body) associated with ↑ expression (r=0.32, P=9.62×10 −4 ).

Techniques: DNA Methylation Assay, Biomarker Discovery, Methylation, Control, Microarray, Expressing, Mass Spectrometry