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A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate

ABSTRACT: We report the comprehensive sequencing of small RNA libraries created from different developmental stages of the basal chordate, Ciona intestinalis. Surprisingly, half of the identified miRNA loci encode not two, but up to four distinct small RNAs. These additional RNAs, termed “moRs”, are generated from sequences adjacent to the predicted ~60-nt pre-miRNA. moRs appear to be produced by RNAse-III-like processing, are ~20-nt in length, have 5’-monophosphate and 3’-hydroxl termini, and like miRNAs, are developmentally regulated.

ORGANISM(S): Ciona intestinalis Drosophila melanogaster

PROVIDER: GSE13625 | GEO | 2009/01/18

SECONDARY ACCESSION(S): PRJNA110655

REPOSITORIES: GEO

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A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate

Project description:We report the comprehensive sequencing of small RNA libraries created from different developmental stages of the basal chordate, Ciona intestinalis. Surprisingly, half of the identified miRNA loci encode not two, but up to four distinct small RNAs. These additional RNAs, termed M-bM-^@M-^\moRsM-bM-^@M-^], are generated from sequences adjacent to the predicted ~60-nt pre-miRNA. moRs appear to be produced by RNAse-III-like processing, are ~20-nt in length, have 5M-bM-^@M-^Y-monophosphate and 3M-bM-^@M-^Y-hydroxl termini, and like miRNAs, are developmentally regulated. Sequencing of small RNA libraries from 4 stages of Ciona intestinalis. Ciona_LarvaMir309_RNASeq and Dmel_Toll10b_RNASeq are sequencing runs to detect if the expression of these RNA products is specific to Ciona or not. An ectopic transcript of the Drosophila melanogaster miR-309 locus was expressed in Ciona to see if it processed the miRs differently than Drosophila melanogaster. The Dmel sequence is from the endogenous case and is a control for comparison.

2009-01-18 | E-GEOD-13625 | biostudies-arrayexpress

Quantitative Multi-Omics Atlas of the Model Chordate Ciona

Project description:We present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ~7k translated genes as well as a deep quantitative atlas of maternal proteins found in the Ciona egg.

2023-11-28 | PXD043619 | Pride

small RNA sequencing of two developmental stages of Ciona intestinalis

Project description:We report the comprehensive sequencing of small RNA libraries created from different developmental stages (larva and gastrula) of the basal chordate, Ciona intestinalis. These libraries were used for the identification of microRNAs in this organism. Sequencing of small RNA libraries from 2 stages of Ciona intestinalis.

2010-03-27 | E-GEOD-21078 | biostudies-arrayexpress

Gata.a, Tcf7 and Zic-r.a ChIP-chip analysis in Ciona intestinalis embryo (16-cell stage)

Project description:DNA binding profiles of three maternal factors (Tcf7, Gata.a and Zic-r.a) in chordate 16-cell stage embryo. 16-cell stage ciona intestinalis embryos were collected from multiple batches and the extracted chromatin was immunoprecipitated by the antibodies which specifically recognize ciona Gata.a, Tcf7 and Zic-r.a, respectively.

2016-04-22 | GSE70902 | GEO

A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate

Project description:A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate

| PRJNA110655 | ENA

small RNA sequencing of two developmental stages of Ciona intestinalis

2010-03-27 | GSE21078 | GEO

The formation of the intestine at the juvenile stage is raised by the Hox10 gene through the migration of endodermal strand cells in ascidian

Project description:Hox cluster genes play crucial roles in the establishment of the body plan along the antero-posterior axis during animal development. Hox genes are expressed in the chordate endodermal tissues, and unraveling functions there is necessary for elucidating the mechanisms of endoderm specification. In the invertebrate chordate Ciona intestinalis, the endodermal tissues are in the premature state at the larval stage, and they form the differentiated digestive tract during metamorphosis. In this study, we showed that a Hox gene Ci-Hox10 is required for the formation of the intestine during metamorphosis. To know the downstream genes that are controlled by Hox10, microarray analysis of Hox10 knock-down embryos was performed. Gene expressions in the tail region of Hox10 knockdown embryos that were injected with Hox10 morpholino (MO) and control embryos of Ciona intestinalis were examined by comparative analysis with two color detection. Dye-swap analysis was carried out.

2013-10-01 | E-GEOD-45475 | biostudies-arrayexpress

Single-cell transcriptome profiling of the Ciona larval brain

Project description:The tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS of vertebrates, sharing many conserved developmental processes, anatomical compartments, neuron subtypes, and even specific neural circuits. Thus, the Ciona tadpole offers a unique opportunity to understand the development and wiring of a chordate CNS at single-cell resolution. Here we report the use of single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. We have also compared these profiles to bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression. Taken together, these datasets have begun to reveal the compartment- and cell-specific gene expression patterns that define the organization of the Ciona larval brain.

2018-10-26 | GSE121807 | GEO

Transcriptome analysis of Ciona intestinalis to identify genes expressed in the adult organs.

Project description:Among urochordates (tunicates)âthe closest living relatives of vertebratesâCiona intestinalis is increasingly being used as a model organism in the field of developmental biology. Ciona intestinalis is the seventh animal which genome published; the ~120-Mbp euchromatin region is estimated to contain ~16,000 protein-coding genes. In addition, analyses of more than one million ESTs have provided the foundation for gene models and associated transcriptomes. The fertilized Ciona intestinalis egg develops into a tadpole larva with a simplified chordate body plan, and then it metamorphose into adult sea squirt of sessile filter feeder. One of interests in the field of developmental biology is to understand what kind of genes are expressed in the body and how spatially and/or temporally coordinated expression of genes is controlled. In this study, we investigated the entire gene expression of 11 organs of adult Ciona; the neural complex, branchial sac, esophagus, stomach, endostyle, intestine, body-wall muscle, heart, blood cells, ovary, and testis. Our data would provides basic information of transcriptome in each organ and help to understand gene expression control of organ specific genes. Gene expressions in 11 organs of adult Ciona intestinalis; blood cells, branchial sac, digestive grand, endostyle, esophagus, heart, body-wall muscle, neural complex, ovary, stomach and testis. Three independent experiments were performed at each tissue using different individuals for each experiment.

2010-10-27 | E-GEOD-24941 | biostudies-arrayexpress

Comparisons of transcriptome of Ciona intestinalis between eggs and 32-cell stage embryos to identify rapidly degrading maternal mRNA

Project description:A genome decoded chordate Ciona intestinalis is one of the suitable animal for analyzing genetic controls in early embryogenesis and zygotically expressed genes are especially intensely studied. However maternally expressed genes are less studied than zygotic ones because of their huge numbers. These microarray experiments were carried out to screen rapidly degrading mRNA to identify crucial maternal mRNAs for Ciona embryogenesis in relatively a short period before their degradation.

2010-12-04 | GSE25817 | GEO

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