Transcriptomics

Dataset Information

237

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. Total RNA from a number of stages across development were pooled and used in a modified DeepCAGE protocol. A custom designed spliced-leader primer (using the SL exon) was used in the 2nd strand synthesis step.

ORGANISM(S): Oikopleura dioica  

SUBMITTER: Coen Campsteijn   J R Manak  Martina Raasholm  Abby M Long  Boris Lenhard  Gemma B Danks  Eric Thompson 

PROVIDER: E-GEOD-50849 | ArrayExpress | 2015-01-26

SECONDARY ACCESSION(S): GSE50849SRP029930PRJNA219164

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Trans-splicing and operons in metazoans: translational control in maternally regulated development and recovery from growth arrest.

Danks Gemma B GB   Raasholm Martina M   Campsteijn Coen C   Long Abby M AM   Manak J Robert JR   Lenhard Boris B   Thompson Eric M EM  

Molecular biology and evolution 20141217 3


Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced-leader (SL) RNA. Trans-splicing also occurs at monocistronic transcripts. The phlyogenetically sporadic appearance of trans-splicing and operons has made the driving force(s) for their evolution in metazoans unclear. Previous work has proposed that germline expression drives operon organization in Caenorhabditis elegans, and a recent hypothesis proposes that operons provide an evolutionary advantage via  ...[more]

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