RNA
Basal Splicing Factors Regulate the Stability of Mature mRNAs in Trypanosomes*

https://doi.org/10.1074/jbc.M112.416578Get rights and content
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Gene expression in trypanosomes is mainly regulated post-transcriptionally. Genes are transcribed as polycistronic mRNAs that are dissected by the concerted action of trans-splicing and polyadenylation. In trans-splicing, a common exon, the spliced leader, is added to all mRNAs from a small RNA. In this study, we examined by microarray analysis the transcriptome following RNAi silencing of the basal splicing factors U2AF65, SF1, and U2AF35. The transcriptome data revealed correlations between the affected genes and their splicing and polyadenylation signaling properties, suggesting that differential binding of these factors to pre-mRNA regulates trans-splicing and hence expression of specific genes. Surprisingly, all these factors were shown to affect not only splicing but also mRNA stability. Affinity purification of SF1 and U2AF35 complexes supported their role in mRNA stability. U2AF35 but not SF1 was shown to bind to ribosomes. To examine the role of splicing factors in mRNA stability, mutations were introduced into the polypyrimidine tract located in the 3′ UTR of a mini-gene, and the results demonstrate that U2AF65 binds to such a site and controls the mRNA stability. We propose that transcripts carrying splicing signals in their 3′ UTR bind the splicing factors and control their stability.

Background: Trypanosome trans-splicing depends on basal splicing factors such as U2AF35, U2FA65, and SF1.

Results: Transcriptome analyses of RNAi-silenced cells of basal splicing factors reveal differential reliance on factors for trans-splicing and a role for the splicing factors in mRNA stability.

Conclusion: Basal splicing factors regulate trans-splicing and mRNA stability.

Significance: This is the first study to suggest that basal splicing factors regulate mRNA stability.

mRNA
Proteomics
Spliceosome
Transcriptomics
Trypanosoma brucei
Trypanosome
Basal Splicing Factors
mRNA Stability
Proteomics of Splicing Complexes

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*

This work was supported in part by the Deutsche Forcshungsgemeinschaft via Deutsche-Israelische Projektkooperation and the Israel Science Foundation.

This article contains supplemental S-1–S-4 and additional references.

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Supported by the Human Frontier Science Program.