Journal: PLoS ONE

Article Title: DNA Methylation Signatures Triggered by Prenatal Maternal Stress Exposure to a Natural Disaster: Project Ice Storm

doi: 10.1371/journal.pone.0107653

Figure Lengend Snippet: Heatmap represents the DNA methylation levels of 500 CGs most significantly associated with objective PNMS (Storm32 score) in 34 donors. Each column represents an individual and each row a single CG. Each cell represents the CG methylation level for one site in one sample. A color gradient intensity scale at the lower right-hand corner of the Heatmap expresses methylation changes. The darkest green indicates the lowest methylation level (Beta-value = 0), the gray indicates the median score (Beta-value = 0.5) and the darkest red indicates the highest methylation level (Beta-value = 1). The color bar on the top of the Heatmap indicates subjects' categorization by their mother's objective PNMS. A color gradient intensity scale at the higher right-hand corner of the Heatmap shows the level of objective PNMS. The darkest blue indicates the lowest objective PNMS (Storm32 score = 5), the gray indicates the median objective PNMS (Storm32 score = 11) and the darkest red indicates the highest objective PNMS (Storm32 score = 21).

Article Snippet: Validation of the 450 K BeadChip Array DNA methylation data was performed with pyrosequencing of bisulfite-treated DNA in 36 youth.

Techniques: DNA Methylation Assay, Methylation

Journal: Clinical Epigenetics

Article Title: DNA hypermethylation contributes to colorectal cancer metastasis by regulating the binding of CEBPB and TFCP2 to the CPEB1 promoter

doi: 10.1186/s13148-021-01071-z

Figure Lengend Snippet: TFCP2 binds to the core TF-binding region of CPEB1 when it is hypermethylated. a Silver staining of the nucleoproteins identified in DNA pull-down assay under various conditions. p-WT, the non-methylated CPEB1 promoter; p-Me, the hypermethylated CPEB1 promoter; control, magnetic beads without probes; Input, total nucleoproteins extracted from HCT116 cells; M, protein molecular mass marker. b WB detecting immunoreactive CEBPB in the nucleoprotein fraction after DNA pull-down with the anti-CEBPB antibody. The molecular mass of CEBPB is approximately 35 kDa. c EMSA revealed that CEBPB protein was unable to bind to its target sequence in the hypermethylated TF-binding region of CPEB1 ; 50 × cold probe WT, 50-fold concentration of the unlabelled wild-type CPEB1 promoter which was served as the competitor probe; Bio-Probe WT, a biotin-labelled wild-type probe of CPEB1 upstream region; Bio-Probe Mut, a biotin-labelled mutant probe of CPEB1 upstream region; Nucleoprotein, nucleoprotein extracted from HCT116 cells; Me-Bio Probe WT, a biotin-labelled hypermethylated probe of CPEB1 upstream region. d TFCP2 may be a candidate methylation reader at the upstream region of CPEB1 ; Methylation, the hypermethylated CPEB1 upstream region probe; Wild-type, the wild-type CPEB1 upstream region probe; Control, a probe with a scrambled sequence of CPEB1 upstream region; TF, the TFs capable of binding to the CPEB1 upstream as determined by ChIP-Seq. e Competitive EMSA to confirm TFCP2 as a methylation reader for CPEB1 . Bio-probe, a biotin-labelled wild-type CPEB1 upstream region probe; Me-Bio Probe, a biotin-labelled hypermethylated CPEB1 upstream region probe; 50 × Cold Probe, 50-fold concentration of the unlabelled wild-type CPEB1 upstream region probe that served as a competitor of the Bio-probe; 50 × Cold Me-Probe, 50-fold concentration the unlabelled hypermethylated CPEB1 upstream region probe that served as a competitor of the Me-Bio Probe

Article Snippet: Publicly available high-throughput DNA methylation microarray data (Illumina Human Methylation 450 K) of 387 CRC tumours and 45 samples of para-tumour tissue were obtained from the TCGA database (level-3).

Techniques: Binding Assay, Silver Staining, Pull Down Assay, Methylation, Control, Magnetic Beads, Marker, Sequencing, Concentration Assay, Mutagenesis, ChIP-sequencing