Several different sequences are implicated in bloodstream-form-specific gene expression in Trypanosoma brucei

Tshitenge, Tania Bishola; Reichert, Lena; Liu, Bin; Clayton, Christine

doi:10.1371/journal.pntd.0010030

Cited by 3 publications

(3 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, the short and medium mRNAs were more than fourfold more abundant in the cytoplasm than in the nucleus at most time points, indicating that their export was unaffected by DRBD18 depletion. We know that reporter mRNAs with shortened RBP10 3′-UTRs can be translated ( Bishola Tshitenge et al 2022 ), so the reduced amount of RBP10 protein after DRBD18 RNAi ( Fig. 1 B) is probably caused by the decrease in total cytosolic RBP10 mRNA ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…We know that reporter mRNAs with shortened RBP10 3'-UTRs can be translated (Bishola Tshitenge et al 2022), so the reduced amount of RBP10 protein after DRBD18 RNAi (Figure 1B) is probably caused by the decrease in total cytosolic RBP10 mRNA (Figure 4C,D).…”

Section: Composition and Associations Of Proteins Of Drbd18 Mrnpsmentioning

confidence: 99%

“…For example, RBP10 (Tb927.8.2780), which is exclusively expressed in mammal-infective forms ( Wurst et al 2012 ; Savage et al 2016 ; Christiano et al 2017 ; Shi et al 2018 ; Vigneron et al 2020 ) specifically associates with procyclic-specific mRNAs, targeting them for destruction ( Mugo and Clayton 2017 ). The RBP10 3′-UTR is 7.3 kb long and contains at least six different regions that are independently capable of causing bloodstream-form-specific expression of a reporter ( Bishola Tshitenge et al 2022 ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns

Tshitenge

Clayton

2022

RNA

Self Cite

View full text Add to dashboard Cite

The parasite Trypanosoma brucei grows as bloodstream forms in mammals, and as procyclic forms in tsetse flies. Transcription is polycistronic, all mRNAs are trans spliced, and polyadenylation sites are defined by downstream splicing signals. Expression regulation therefore depends heavily on post-transcriptional mechanisms. The RNA-binding protein DRBD18 was previously implicated in the export of some mRNAs from the nucleus in procyclic forms. It copurifies the outer ring of the nuclear pore, mRNA export factors and exon-junction-complex proteins. We show that for more than 200 mRNAs, DRBD18 depletion caused preferential accumulation of versions with shortened 3′-untranslated regions, arising from use of polyadenylation sites that were either undetectable or rarely seen in nondepleted cells. The shortened mRNAs were often, but not always, more abundant in depleted cells than the corresponding longer versions in normal cells. Their appearance was linked to the appearance of trans-spliced, polyadenylated RNAs containing only downstream 3′-untranslated region-derived sequences. Experiments with one mRNA suggested that nuclear retention alone, through depletion of MEX67, did not affect mRNA length, suggesting a specific effect of DRBD18 on processing. DRBD18-bound mRNAs were enriched in polypyrimidine tract motifs, and DRBD18 was found in both the nucleus and the cytoplasm. We therefore suggest that in the nucleus, DRBD18 might bind to polypyrimidine tracts in 3′-UTRs of mRNA precursors. Such binding might both prevent recognition of mRNA-internal polypyrimidine tracts by splicing factors, and promote export of the processed bound mRNAs to the cytosol.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Composition and Associations Of Proteins Of Drbd18 Mrnpsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns

Tshitenge

Clayton

2022

RNA

Self Cite

View full text Add to dashboard Cite

show abstract

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

Trenaman,

Tinti,

Wall

et al. 2024

Nat Commun

View full text Add to dashboard Cite

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.

show abstract

Life stage–specific poly(A) site selection regulated byTrypanosoma bruceiDRBD18

Bard,

Tylec,

Dubey

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The kinetoplastid parasite, Trypanosoma brucei , undergoes a complex life cycle entailing slender and stumpy bloodstream forms in mammals and procyclic and metacyclic forms (MFs) in tsetse fly hosts. The numerous gene regulatory events that underlie T. brucei differentiation between hosts, as well as between active and quiescent stages within each host, take place in the near absence of transcriptional control. Rather, differentiation is controlled by RNA-binding proteins (RBPs) that associate with mRNA 3′ untranslated regions (3′UTRs) to impact RNA stability and translational efficiency. DRBD18 is a multifunctional T. brucei RBP, shown to impact mRNA stability, translation, export, and processing. Here, we use single-cell RNAseq to characterize transcriptomic changes in cell populations that arise upon DRBD18 depletion, as well as to visualize transcriptome-wide alterations to 3′UTR length. We show that in procyclic insect stages, DRBD18 represses expression of stumpy bloodstream form and MF transcripts. Additionally, DRBD18 regulates the 3′UTR lengths of over 1,500 transcripts, typically promoting the use of distal polyadenylation sites, and thus the inclusion of 3′UTR regulatory elements. Remarkably, comparison of polyadenylation patterns in DRBD18 knockdowns with polyadenylation patterns in stumpy bloodstream forms shows numerous similarities, revealing a role for poly(A) site selection in developmental gene regulation, and indicating that DRBD18 controls this process for a set of transcripts. RNA immunoprecipitation supports a direct role for DRBD18 in poly(A) site selection. This report highlights the importance of alternative polyadenylation in T. brucei developmental control and identifies a critical RBP in this process.

show abstract

Several different sequences are implicated in bloodstream-form-specific gene expression in Trypanosoma brucei

Cited by 3 publications

References 70 publications

The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns

The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns

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

Life stage–specific poly(A) site selection regulated byTrypanosoma bruceiDRBD18

Contact Info

Product

Resources

About