Trypanosome bromodomain proteins maintain a BF-specific transcriptome.

(A) Volcano plot showing the most significant up- and down-regulated genes in the trypanosome genome from an RNA-seq experiment comparing cells treated for 3 d with I-BET151 to control DMSO-treated cells. DESeq was used to normalize counts, compute log2(fold change) of treated cells over untreated cells, and calculate p-adjusted values. Dots in red indicate genes with fold changes of > 2 and a p-adjusted value 2(RPKM) values for all genes within hierarchically clustered groups previously shown to be differentially expressed in the transition from BF to PF [12]. Each cluster is demarcated by alternating white and gray shading and contains 3 boxplots representing DMSO-treated, 2d I-BET151-treated, and 3d I-BET151-treated cells. All clusters with a Gene Set Enrichment Analysis (GSEA) false discovery rate (FDR) 70% of genes up- or down-regulated within each cluster at 48 h postinduction are shown. The median for each set of genes is shown as a red line. Whiskers demarcate the inner quartile range. Outliers are shown as blue dots. (D) Boxplots as in C except that the genes previously shown to be differentially expressed upon differentiation from the BF to the PF are now grouped in the indicated pathways. ISG, invariant surface glycoproteins, Glyc, glycosomal enzymes, mit CAC, mitochondrial citric acid cycle, glycBS, proteins required for high rate of glucose and glycerol metabolism in BFs, GPI, Glycosyl phosphatidylinosotol metabolism, cyc, cell cycle, flag, flagellar genes, procyc, procyclic surface antigens, cyskel, cytoskeletal genes, vestrans, proteins required for intracellular protein and vesicular transport. (E and F) DESeq was used to call genes with significantly altered transcription between I-BET151 treated cells and DMSO-treated control cells for every time point using a p-adjusted cutoff of S1 Data.