Fig. 3
Top ranking promoter regions included imprint regulator gene ZFP57. a Top 5 differentially methylated regions (DMR) at promoters, sorted by combined RnBeads rank (smallest to largest) as for Fig. 2d above, except combining values across all the CpG sites in the DMR as detailed in the “Methods” section. Abbreviations as above except # probes, number of probes on EPIC array included in DMR. b Top: genome browser tracks showing the region around the DMR upstream of ZFP57, genomic coordinates in hg19 human genome release, and scale as shown. EPIC array probes showing differential methylation (blue, gain; red, loss) are indicated, with size indicating the magnitude of change. The start of the ZFP57 gene and the position of the pyrosequencing assay (Pyro) are also shown. Δβ, mean difference in β value between placebo and FA-treated groups; maximum gain and loss also shown (+ 0.09 β = 9% methylation). Bottom: Loess plot of β values across the region, with CpG identification numbers from array below; those forming the DMR defined by RnBeads are indicated, as well as sites analyzed by pyroassay. Each dot represents β value in an individual sample, with lines representing smoothed averages; color code is indicated at left. c Results of pyroassay covering the six sites indicated in b. Sample groups: cord blood DNA from placebo (n = 45) and FA-treated (n = 41). Mean, average of the individual means in that group; Max., largest of the mean methylation values in that group; Min, lowest mean in group; SD, standard deviation for the means; Change, difference in % methylation seen between groups; P, probability (Student’s t test)