Fig. 4a–d

Effects of ZC3H41 depletion on the transcriptome of procyclic Trypanosoma brucei. a Volcano plot of differential gene expression in ZC3H41-depleted cells compared to control cells. Blue dots correspond to downregulated transcripts, orange dots indicate upregulated transcripts, and grey dots represent unregulated messenger RNAs (mRNAs); thresholds for differential abundance were |log2 fold change|> 1 and false discovery rate < 0.01. b, c Coverage plots of ZC3H41 and Tb927.11.11410 loci. Read counts were analyzed with sliding windows (100-base pair bins, 10-base pair steps) and normalized by library size (reads per million). Open-reading frames are represented as thick, filled boxes, untranslated regions as thin, open boxes; arrows indicate the direction of transcription. Reads per million values are represented as the mean (solid lines) ± SEM (shaded area) of three RNA-seq biological replicates. d Quantitative reverse transcription–polymerase chain reaction (RT-PCR) analysis to confirm proper ablation of ZC3H41 mRNA and upregulation of trans-sialidase (TS) transcript. Fold changes (log2 converted) are expressed as the mean (horizontal lines) ± SEM (shaded areas) of three independent RNAi inductions in procyclic trypanosomes (dots). The horizontal dashed line indicates log2 = 0, i.e. no change in gene expression