Fig. 2

PLD3 DNA methylation levels in human hippocampal samples. a The graph shows genomic position of the amplicons (black boxes) validated by bisulfite cloning sequencing which contain the cytosines assayed by pyrosequencing (CpG1 and CpG2) within the promoter regions (principal and alternative) of the PLD3 gene. PLD3 is located on the long arm of chromosome 19 (chr19:40,854,332-40,884,390 -GRchr19/hg19 coordinates). CpG islands are represented by isolated green boxes. At the bottom of the graph, predicted functional elements are shown for each of nine human cell lines explored by chromatine imunoprecipitation (ChIP) combined with massively parallel DNA sequencing. Boxes represent promoter regions (red), enhancers (yellow), transcriptional transition and elongation (dark green), and weak transcribed regions (light green). The track was obtained from the Chromatin State Segmentation by HMM from ENCODE/Broad track shown at the UCSC Genome Browser. b Dot-plot charts representing methylation levels for principal and alternative promoter of PLD3 by pyrosequencing. Horizontal lines represent median methylation values for each group.*p value < 0.05. c Representative examples of bisulfite cloning sequencing validation for the two independent amplicons (principal and alternative promoter regions). Black and white circles denote methylated and unmethylated cytosines respectively. Each column symbolizes a unique CpG site in the examined amplicon, and each line represents an individual DNA clone