Fig. 1

FMR1 locus (h)MeDIP profiling identifies novel regions of 5mC and 5hmC changes in FXS patient PBMC samples. a. Experimental overview. Methylated DNA immunoprecipitation (MeDIP) assay was used to profile DNA methylation (5mC), DNA hydroxymethylation (5hmC). Chromatin immunoprecipitation (ChIP) was used to profile histone post-translational modifications (PTM). Antibody (Ab) b–c. The graphs illustrate the relative enrichment of the indicated mark (log2 fold enrichment) in FXS (red) and control (blue) PBMCs. The upper panel illustrates the chromosomal and genomic location locations as well as the indicated referenced Refseq genes: FMR1, and referenced antisense non coding RNAs (FMR1AS1 and L29074.3). This snapshot illustrates the epigenetic landscape over a region covering 79 kb on ChrX: 146971000-147050000 (c). RPL19 and GAPDH provide controls regions of no changes in 5mC and 5hmC (b). In the graphs, the thicker lines indicate higher deviation between biological replicates (controls n = 4; FXS n = 8) (aggregation mean, sliding window 529 bp). Regions I to V were selected as regions of strongest apparent epigenetic variation across epigenetic marks and cell types based on epigenomic landscape visualization illustrated in Figs. 1 and 3. The chromosome coordinates of these regions are provided in Table 1