Oikopleura dioica
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ABSTRACT:
PROVIDER: PRJNA313934 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica
| PRJNA219164 | ENA
Project description:ChIP-seq was used to generate chromatin state maps, profile binding patterns of key architectural proteins and locate putative enhancer regions in the early development (TB stage) and developing gonads of the marine chrodate Oikopleura dioica.
2021-04-21 | GSE172470 | GEO
Project description: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.
2015-01-26 | E-GEOD-50849 | biostudies-arrayexpress
Project description:The selection and activity of transcription start sites (TSSs) are central to gene regulation and depend on sequence and chromatin features within a core promoter region. We present, at single-bp resolution, the TSS landscape of Oikopleura dioica, a marine chordate in the sister group to vertebrates and relate dynamics of promoter usage, and their architectures, across its life cycle, to chromatin features. TSS selection grammars include a genome-wide shift during spermatogenesis to promoters with a novel, position-specific, core promoter element, present in >70% of male-specific promoters. Differential promoter usage in spermatogenesis includes the activation of cryptic internal promoters within polycistronic operons, alternative TSS selection within promoters of genes expressed in earlier development and the exclusion of trans-splice sites. In contrast, maternal promoters, which are active in endocycling nurse nuclei in O. dioica, lack position-specific motifs, have dispersed TSS usage, ordered nucleosomes around the TSS and typical histone modifications associated with broad promoters. Furthermore, our results indicate that the cell cycle regulator, E2F1, acts as a master regulator of these maternally expressed genes. Zygotic promoters are also predominantly broad and the vertebrate maternal to zygotic switch in mode of TSS-selection is absent. DNA methylation in gene bodies is an ancient property of eukaryotic genomes and is thought to repress alternative TSSs. We report a strong association between gene body DNA methylation, H3K4me3-depletion and TATA-dependent sharp promoters in O. dioica. Core promoter features may therefore determine the subset of gene bodies that are methylated in this invertebrate genome.
2018-02-05 | GSE78794 | GEO
Project description: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.
2015-01-26 | GSE50849 | GEO
Project description:Oikopleura dioica (Japan) Transcriptome or Gene expression
| PRJNA269316 | ENA
Project description:Developemtanl transcriptomes of an appendicularian, Oikopleura dioica.
| PRJDB5668 | ENA
Project description:Oikopleura dioica (Japan) Transcriptome or Gene expression
| PRJNA269215 | ENA
Project description:In multicellular organisms, histone posttranslational modifications plays roles in transitions associated with the cell cycle, development, germline specification, gametogenesis and inheritance. Here we defined adaptations of an epigenome in tunicates, sister group to vertebrates, to strong secondary genome compaction in the larvacean, Oikopleura dioica, that has separate sexes and male heterogamy. We profiled 19 histone post-translational modifications in homogeneous ovary and testis samples and used the combinatorics of these marks to define chromatin states. We supplemented these with profiles of RNA polymerase II, CTCF and p300 binding sites and integrated existing annotation and expression data to characterize distinct epigenomic landscapes of the ovary and testis.
2017-01-26 | GSE78915 | GEO