Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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: Eric Thompson

PROVIDER: E-GEOD-50849 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

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]

PMID: 25525214

Similar Datasets

Project description:Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). We integrated CAGE-seq, ChIP-seq and gene expression profiles to discover shared or cell-specific regulatory elements, transcription start sites and transcripts associated to the transition from pluripotent to neural-restricted stem cell. Our analysis showed that >90% of the promoters are in common between the two cell types, while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provide a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and gene expression programs occurring in the transition from a pluripotent to a neural-restricted cell fate. Investiagtion of promoters usage changes during ESCs neural induction ESCs and NESCs promoter usage profiling by CAGE-seq

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.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure