While regulatory programs are extensively studied at the level of transcription, elements that are involved in regulation of post-transcriptional processes are largely unknown, and methods for systematic identification of these elements are in early stages. Here, using a novel computational framework, we have integrated sequence information with several functional genomics data sets to characterize conserved regulatory programs of trypanosomatids, a group of eukaryotes that almost entirely rely on post-transcriptional processes for regulation of mRNA abundance. This analysis revealed a complex network of linear and structural RNA elements that potentially govern mRNA abundance across different life stages and environmental conditions. Furthermore, we show that the conserved regulatory network that we have identified is responsive to chemical perturbation of several biological functions in trypanosomatids. We have further characterized one of the most abundant regulatory RNA elements that we discovered, an AU-rich element (ARE) that can be found in 3′ untranslated region of many trypanosomatid genes. Using bioinformatics approaches as well as in vitro and in vivo experiments, we have identified three ELAV-like homologs, including the developmentally critical protein TbRBP6, which regulate abundance of a large number of trypanosomatid ARE-containing transcripts. Together, these studies lay out a roadmap for characterization of mechanisms that modulate development and metabolic pathways in trypanosomatids.

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Trypanosoma brucei, the causative agent of African sleeping sickness, contains a single mitochondrion which imports proteins responsible for RNA editing process. Using RNA interference (RNAi), this study aims to characterize the gene Tb 11.02.1480, annotated as mitochondrial processing peptidase α‐subunit (MPP‐α) that is believed to cleave mitochondrial import signal to aid protein maturation. Severe growth inhibition resulted from RNAi. Analysis of transcript level by RT‐PCR showed a 2–8 fold accumulation in pre‐edited mRNAs that encode electron transport chain components apocytochrome b, ATP synthase subunit 6 and NADH‐ubiquinone oxidoreductase subunit 3 (ND3), along with relatively unchanged levels of never‐edited mRNAs ND4 and cytochrome oxidase 1. Mitochondrial extract prepared from glycerol gradient fractionation suggest disruption of editosome integrity, although maturation of editosome subunit KREL1 was unaffected. These observations suggest that the proposed MPP‐α in T brucei might not be involved in protein import as reported in other species; but impaired RNA editing activity suggest this protein contributes to editosome stability. This was supported by computational analysis where this protein appears to interact with editosome accessory proteins MRP. Ongoing work on identification of protein interacting partners would allow further elucidation of gene function.