<p>(A) Methylation-specific PCR (MSP) analyses using <i>Dpn</i>II or <i>Bfu</i>CI showing that <i>disiRNA</i> loci are methylated. CD and CB are samples that were only treated with either <i>Dpn</i>II or <i>Bfu</i>CI restriction digestion buffer, respectively. <i>ζ-η</i> and <i>ncu06312</i> gene regions were used as positive (methylated) and negative (unmethylated) controls, respectively. Primer pair 113–114 covers a region without DpnII/BfuCI recognition sites. Agarose gel images show the results of semi-quantitaive PCR analyses. The estimated percentages of methylation (right) for these loci were determined by qPCR. (B) Correlation between DNA methylation level (upper panel) and disiRNA expression profile (low panel) spanning the <i>disi-47</i> locus as determined by MSP using qPCR. The <i>am</i> locus served as a negative control. (C) Correlation between DNA methylation level and disiRNA expression profile at the <i>disi-6</i> locus determined by MeDIP. Arrows indicate the locations of primer pairs (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003761#pgen.1003761.s001" target="_blank">Figure S1</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003761#pgen.1003761.s009" target="_blank">Table S1</a> for primer information).</p
