To validate signals observed on our microarray and differences between High and Low LG offspring, we quantified changes in H3K9 acetylation, DNA methylation, and transcription. H3K9 acetylation differences in 7 regions ( Fig. 1a ) and DNA methylation differences in 12 regions ( Fig. 1b ) were validated by quantitative PCR (qChIP – see Methods for details; [21]). Levels of DNA methylation validated by qChIP correlated significantly with levels of enrichment detected by microarray (R = 0.38, P = 0.0029 by Pearson's correlation; Fig. S1). DNA methylation differences were further confirmed for four genes by sequencing sodium bisulfite converted DNA (Fig. S2). False positives due to DNA polymorphism rather than differential methylation were ruled out for 12 regions (those validated by qChIP above) via DNA sequencing (data not shown). Of nine genes showing significant differences in gene expression between High and Low LG offspring, all were significantly more expressed among High LG offspring ( Fig. 1c ).
