<p>(A and B) MeDIP results showing the DNA methylation status of the <i>ccg-1</i> promoter, <i>luc</i> gene body, and the <i>qa-2</i> promoter of the indicated construct. The artificial construct <i>Pqa-2:cul:1-gccP</i> (A) or <i>Pqa-2:cul</i> (B) resides at the <i>his-3</i> locus. The top cartoon of each panel depicts the architecture of the construct and black bars indicate the approximate location of primer sets. Three independent repeats were performed. Values are mean ± s.d. (C) Distribution of DNA methylation at the endogenous location of the <i>qa-2</i> promoter of the <i>Pqa-2:cul:1-gccP</i> strain. (D) Distribution of DNA methylation around the <i>Pqa-2:cul:1-gccP</i> construct at the <i>his-3</i> locus with/without the activation of the <i>qa-2</i> promoter. In panels A-D, QA+ and QA- indicate presence or absence of quinic acid (QA), respectively. DNA methylation was measured with MeDIP. (E) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003761#s2" target="_blank">Results</a> of bisulfite PCR in the region upstream of the <i>qa-2</i> promoter of the <i>Pqa-2:cul:1-gccP</i> construct. Two aliquots of genomic DNA from <i>Pqa-2:cul:1-gccP</i> strain, one digested with <i>Bfu</i>CI and one untreated, were subject to bisulfite treatment and sequencing, respectively (strategy 2 of bisulfite sequencing, primer sequences in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003761#pgen.1003761.s012" target="_blank">table S4</a>). Each row of circles represents the order and number of cytosines in the subcloned sequence. Opened and filled circles indicate unmethylated and methylated cytosine, respectively.</p
