Fig. 4
Genome-wide nucleosomal organization in BF and PF T. brucei. a Chromosome 6 is selected as example, and statistically significant differences between BF and PF stages are shown. The top line indicates the position of assigned genes on the Watson strand (above horizontal axis) and the Crick strand (below horizontal axis). The location of the centromere is indicated by the filled circle. The yellow line shows the A/T % at each setting of a 100-bp scanning window. The black traces below show the traces of the log2 ratio of the average number of assigned dyad axes in a 1000-bp scanning window to the genome average in either BF or PF. The correlation between the relative nucleosome density in BF and PF chromatin was calculated by the Whitney–Mann U test at 50-bp intervals in a 500-bp sliding window. The number of statistically significant (p < 0.01) samples in four biological replicates was added and is shown as a “significance” value in the red traces. The small black circles identify peaks of high significance where the nucleosomal organization of the corresponding regions was individually assessed. b The distribution of dyads at the EP1–EP2 procyclin locus (black bars) in a 3500-bp region. In each case, the red and blue impulse plots represent two biological replicates of BF (top panel) and PF (bottom panel) chromatin. c, d Alignment of nucleosomal dyads in chromatin from BF HNI_VO2 cell line. Coding sequences of the neomycin and hygromycin single copy resistance marker genes, present immediately downstream of the pol I ES promoters, were analyzed. Lower levels of well-positioned nucleosomes were present on the active neomycin gene (c), with regions of dyad enrichment observed for the transcriptionally inactive hygromycin gene (d). Y-axes scales are mirrored, with the left-hand y-axes indicating number of enclosed bases (black trace), and the right-hand axes indicating number of dyads (blue)