Effect of the depletion of PuREBP1 (Tb927.4.4550) on the transcriptome of Trypanosoma brucei [RNAi]

We have previously characterized a short RNA stem-loop cis-element within the 3'-UTR of the NT8 nucleobase transporter mRNA (PuRE, Purine Responsive Element) that is necessary and sufficient to confer a strong repression of gene expression in response to purines in the human parasite Trypanosoma brucei (PMID: 24813448). In this study, we have identified a protein complex composed of two RNA-binding proteins (Tb927.4.4550 and Tb927.3.3060, named here as PuREBP1 and PuREBP2 respectively) that binds to the PuRE in vitro and to NT8 mRNA in vivo. Depletion of PuREBP1 by RNAi results in the upregulation of just NT8 and the mRNAs encoding the amino acid transporter AATP6 paralogues. Moreover, we found that the PuREBP1/2 complex is associated with only a handful of mRNAs, and that it is responsible for the observed purine-dependent regulation of NT8 expression. Depletion of PuRBP1 results in the upregulation of just two mRNAs (encoding membrane transporters NT8 and AATP6) and downregulation of four other mRNAs (including the one encoding PuREBP1, as expected) Total RNA was obtained from non-induced (control) vs PuREBP1-depleted trypanosomes after 48h of RNAi induction. Two biological replicates = 4 samples in total