Figure 5.

Visualization of meDIP-seq data mapped to select Oxytricha trifallax chromosomes. (a) 46 hour methylcytosine immunoprecipitation reads mapped to the methylation cohort of eleven chromosomes (Figure 4c, above the dotted line). Read depth is represented by the peaks in the y dimension for each chromosome (scale not comparable between chromosomes). CC motifs are shown as purple arrowheads below the reads for each chromosome. The gold bar represents the ORF, consistently oriented from left to right in all chromosomes. Teal arrows indicate oligos used in bisulfite-PCR, while grey arrows shown above the ORF indicate oligos used in bisulfite-qPCR. (b) Scaled plot of Contig2927.0 meDIP-seq signal, the highest ranking chromosome in both the methylation and hydroxymethylation cohorts, for immunoprecipitation with IgG, methylcytosine (mC) and hydroxymethylcytosine (hmC) in both vegetative (negative control) and 46 h DNA. One million reads from each library were plotted at equal scales, so that the heights of peaks (and read numbers) are directly comparable. (c) Scaled plot of TEBPβ showing enrichment both for methylcytosine (mC) and hydroxymethylcytosine (hmC), with plotting and scaling as in (b). Dark lines under 46 h mC and hmC plots represent the methylated/hydroxymethylated aberrantly spliced product identified by bisulfite-PCR (shown in Figure 6d,e). ORF, open reading frame; qPCR, quantitative PCR; TEBPβ, Telomere End-Binding Protein β; Veg, vegetative.