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

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

PROVIDER: PRJNA110655 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR014353.fastq.gz	Fastqsanger.gz
	SRR014354.fastq.gz	Fastqsanger.gz
	SRR014355.fastq.gz	Fastqsanger.gz
	SRR014356.fastq.gz	Fastqsanger.gz
	SRR014357.fastq.gz	Fastqsanger.gz

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

2009-01-18 | GSE13625 | GEO

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

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

Project description:MicroRNAs (miRNAs) have been implicated in various cellular processes. They are thought to function primarily as inhibitors of gene activity by attenuating translation or promoting mRNA degradation. A typical miRNA gene produces a predominant approximately 21-nucleotide (nt) RNA (the miRNA) along with a less abundant miRNA(*) product. We sought to identify miRNAs from the simple chordate Ciona intestinalis through comprehensive sequencing of small RNA libraries created from different developmental stages. Unexpectedly, half of the identified miRNA loci encode up to four distinct, stable small RNAs. The additional RNAs, miRNA-offset RNAs (moRs), are generated from sequences immediately adjacent to the predicted approximately 60-nt pre-miRNA. moRs seem to be produced by RNAse III-like processing, are approximately 20 nt long and, like miRNAs, are observed at specific developmental stages. We present evidence suggesting that the biogenesis of moRs results from an intrinsic property of the miRNA processing machinery in C. intestinalis.

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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

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Targeting kidney proximal tubules by protein nanocages via glomerular filtration

Project description:Nature exploits cage-like proteins for a variety of biological purposes from molecular packaging and cargo delivery to catalysis. These cage-like proteins are of immense importance in nanomedicine due to their propensity to self-assemble from simple identical building blocks to highly-ordered architecture and the design flexibility afforded by protein engineering. However, delivery of protein nanocages to the renal tubules remains a major challenge because of the glomerular filtration barrier, which effectively excludes conventional size nanocages. Here we show that DNA-binding Protein from Starved cells (Dps)—the extremely small archaeal antioxidant nanocage—is able to cross the glomerular filtration barrier and is endocytosed by the renal proximal tubules. Using a model of endotoxemia, we present an example of the way in which proximal tubule-selective Dps nanocage can limit the degree of endotoxin-induced kidney injury. This was accomplished by amplifying the endogenous antioxidant property of Dps with addition of a dinuclear manganese cluster. Dps is the first-in-class, protein cage nanoparticle that can be targeted to renal proximal tubules through glomerular filtration. In addition to its therapeutic potential, chemical and genetic engineering of Dps will offer a novel nanoplatform to advance our understanding of the physiology and pathophysiology of glomerular filtration and tubular endocytosis.

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Quantitative proteome dynamics across embryogenesis in a model chordate

Project description:The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ~7k translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.

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