Post-transcriptional reprogramming by thousands of mRNA untranslated regions in trypanosomes

• Published in: Nature communications 2024-09, Vol.15 (1), p.8113-18, Article 8113
• Main Authors: Trenaman, Anna, Tinti, Michele, Wall, Richard J., Horn, David
• Format: Article
• Language: English
• Subjects: 3' Untranslated regions; 3' Untranslated Regions - genetics; 38; 38/47; 45; 49; 631/208/199; 631/326/417/2551; Adenine; Cell activation; Gene expression; Gene Expression Regulation; Genome, Protozoan; Genomes; Humanities and Social Sciences; Machine learning; multidisciplinary; Nucleotide sequence; Post-transcription; Regulatory sequences; RNA Processing, Post-Transcriptional; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Protozoan - genetics; RNA, Protozoan - metabolism; Robust control; Science; Science (multidisciplinary); Trypanosoma - genetics; Trypanosoma - metabolism; Trypanosoma brucei brucei - genetics; Trypanosoma brucei brucei - metabolism; Trypanosome; Uracil
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-52432-0

Although genome-wide polycistronic transcription places major emphasis on post-transcriptional controls in trypanosomatids, messenger RNA cis -regulatory untranslated regions (UTRs) have remained largely uncharacterised. Here, we describe a genome-scale massive parallel reporter assay coupled with 3’-UTR-seq profiling in the African trypanosome and identify thousands of regulatory UTRs. Increased translation efficiency was associated with dosage of adenine-rich poly-purine tracts (pPuTs). An independent assessment of native UTRs using machine learning based predictions confirmed the robust correspondence between pPuTs and positive control, as did an assessment of synthetic UTRs. Those 3’-UTRs associated with upregulated expression in bloodstream-stage cells were also enriched in uracil-rich poly-pyrimidine tracts, suggesting a mechanism for developmental activation through pPuT ‘unmasking’. Thus, we describe a cis -regulatory UTR sequence ‘code’ that underpins gene expression control in the context of a constitutively transcribed genome. We conclude that thousands of UTRs post-transcriptionally reprogram gene expression profiles in trypanosomes. Cells that transcribe almost ‘everything everywhere all at once’ rely upon alternative expression controls. Here the authors employ massive parallel reporter assays and 3’UTR-seq to profile regulatory untranslated regions (UTRs) in African trypanosome.