Fig. 5: Expression of promoter-adjacent genes is disrupted in H4^K4Q mutants.

a The schematic illustrates a canonical RNA polymerase II transcribed polycistronic transcription unit in T. brucei, showing the distribution of genes closest to the start-site (orange), closest to a termination-site (blue) and all other genes (grey). The boxplot shows log₂ fold-change in RNA-seq data when we compared three strains expressing the H4^K4Q mutant to an H4^K4K control. Genes within 10 kbp of a transcription start-sites (orange, n = 736), genes within 10 kbp of a termination-site (blue, n = 576), all other genes (grey, n = 8755). Boxes indicate the interquartile range (IQR), the whiskers show the range of values within 1.5 × IQR and a horizontal line indicates the median. The notches represent the 95% confidence interval for each median. p-values calculated using two-sided t-tests. b RNA-seq analysis focussing on genes adjacent to divergent start-sites (top left), genes adjacent to convergent termination-sites (top right), genes adjacent to start-sites where another polycistron ends (bottom left), and genes adjacent to termination-sites where another polycistron starts (bottom right). Distances from the start or end are shown on the x-axis. Numbers of transcripts within 10 kbp of a start- or termination-site that were significantly (FDR < 0.01) increased or decreased in abundance in the H4^K4Q mutant relative to the H4^K4K control are indicated. These numbers were used to calculate p-values using χ² tests. FDR, False Discovery Rate. c The circular plot shows the full RNA-seq dataset mapped to the T. brucei chromosome cores (data in grey). Transcripts from genes that are within 10 kbp of a promoter (black bars, as defined by the upstream borders of H4^K10 acetylation footprints), and that are significantly (FDR < 0.01) increased or reduced in abundance in the H4^K4Q mutant relative to the H4^K4K control, are highlighted.