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Fig. 2 | Clinical Epigenetics

Fig. 2

From: Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

Fig. 2

Inter-individual variation in 5mC and 5hmC levels across the FMR1 locus of FXS patient PBMC samples. a Selected FMR1 genomic regions of methylation change (Table 1) throughout the FMR1 locus were interrogated by (h)MeDIP-PCR in DNA extracted from four control (blue) and eight FXS (red) patient PBMCs samples, data represent the mean of relative enrichment to input in log2 with standard deviation SD (left panels) and individual data for the 2I3-4 locus (right panels). Significance levels of the mean difference in control and FXS PBMCs is indicated by triple asterisks p ≤ 0.001, double asterisks p ≤ 0.01, single asterisk p ≤ 0.05, or no star, p > 0.05 using a t test with unequal variance (Additional file 11: Table S4). The location of qPCR primer pairs (Additional file 9: Table S2) used in this study is illustrated. Data for inter-individual 5mC and 5hmC variation across all selected FMR1 loci is available in Additional file 2: Figure S1 and Additional file 3: Figure S2. Arrows in a, b, and c illustrate observed anti-correlation between 5mC and 5hmC enrichment in two FXS patients samples B and E. b (h)MedIP-array methylation profiles surrounding FMR1 transcriptional start site are represented in eight individual FXS patient samples (A to H in red) as compared to control samples (blue) for 5mC and 5hmC. c Pyrosequencing at the FMR1 promoter region, using a commercial assay (HsFMR1, QIAGEN) located at proximity of the FMR1 start site and a newly designed assay (B3) in a novel region of methylation changes located 738 bp downstream of the TSS confirm DNA methylation enrichment at the base resolution level in all eight patients. The genomic location of measured CpGs relative to the TSS is indicated (see Additional file 10: Table S3)

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