Fig. 2

Histone variants have distinct localization genome-wide. A. Pileups of histone variant ChIP-seq reads mapping to genes of interest. Note, individual nucleosomes can be resolved from this data. Genes shown are tachyzoite genes SAG1, ENO2 and LDH1 and bradyzoite genes BAG1, ENO1 and LDH2. B. The overall similarity in ChIP-seq profiles was compared by calculating Pearson correlation coefficients genome-wide or for different genomic features including promoters, gene bodies and 3′ UTRs (as defined by www.toxodb.org annotations). Correlations were visualized in a clustered heatmap (generated using deeptools http://deeptools.readthedocs.io); color indicates correlation coefficient as shown in color key. Peaks for each variant represent the intersection of peaks from each biological replicate. C. Average ChIP-seq profiles of each histone variant on different genomic features. Start and end denote boundaries of each feature, with 500 bp upstream and downstream flanking sequence either side. ChIP-seq read pileups were normalized by scaling to library size