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Genome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica

ABSTRACT: Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica and find evidence for proposed functions of SL-trans-splicing. A recent hypothesis postulates that operons facilitate recovery from growth arrested states in metazoans. We examined the expression dynamics of operons across the life-cycle of the animal and during growth arrest recovery. We show that operons do not facilitate recovery from growth arrest in O. dioica. We find that operons are enriched in the germline and that trans-spliced transcripts are predominantly maternal., Interestingly, there is a TOP-like motif in the SL sequence, and trans-splicing in TOP mRNAs, indicating that trans-spliced mRNAs are targets for nutrient-dependent translational control in O. dioica.

ORGANISM(S): Oikopleura dioica

PROVIDER: GSE50849 | GEO | 2015/01/26

SECONDARY ACCESSION(S): PRJNA219164

REPOSITORIES: GEO

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Project description:Protein synthesis is an energy-demanding process essential for cell proliferation and survival. Balancing the cost of protein synthesis with available resources has driven the evolution of its nutrient-dependent regulation. A central mechanism in this regulation is the repression of translation of the protein synthesis machinery during unfavorable growth conditions. This is mediated via mammalian target of rapamycin (mTOR), a master regulator of growth conserved from yeast to human. Despite extensive research, and the elucidation of a number of important factors, how mRNAs are translationally regulated by mTOR is still unclear. Repression depends on a 5’ Terminal Oligo Pyrimidine (TOP) motif which is conserved across vertebrates and present in Drosophila melanogaster. In Caenorhabditis elegans and the marine chordate Oikopleura dioica most TOP mRNAs are trans-spliced to a spliced leader. This results in the removal of the originally transcribed 5’ end and its replacement with a common short RNA sequence. In both species the 5’ end of the spliced leader is pyrimidine-enriched but does not meet strict requirements for a canonical TOP motif. How this affects the translational control of TOP mRNAs is unknown. Here, using transcriptome-wide ribosome profiling on whole animals treated with the mTOR inhibitor Torin 1, we show that trans-spliced TOP mRNAs in O. dioica are subject to mTOR-dependent translational control. We also show, using existing data, that trans-spliced transcripts in C. elegans are differentially translated upon recovery from starvation-induced developmental diapause. Together our results demonstrate that spliced leaders in metazoans are targets for mTOR-dependent translational control in response to nutrient availability. This indicates that trans-splicing in metazoans, the function of which has remained largely enigmatic, plays a key role in the coordinated translational regulation of growth-related genes. Moreover, our results reveal an innovative strategy for rapid evolution and developmental control of downstream targets of the ancient mTOR pathway.

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Genome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica

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