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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The Early Origins and Evolution of microRNAs and piRNAs in Animals

ABSTRACT: We explored the potential for small RNA biology in organisms that diverged basal to Bilateria, identifying both miRNAs and piRNAs in Nematsotella and Amphimedon Employ HTS of endogenous small RNAs

ORGANISM(S): Nematostella vectensis

SUBMITTER: andrew grimson

PROVIDER: E-GEOD-12578 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals.

Grimson Andrew A Srivastava Mansi M Fahey Bryony B Woodcroft Ben J BJ Chiang H Rosaria HR King Nicole N Degnan Bernard M BM Rokhsar Daniel S DS Bartel David P DP

Nature 20081001 7217

In bilaterian animals, such as humans, flies and worms, hundreds of microRNAs (miRNAs), some conserved throughout bilaterian evolution, collectively regulate a substantial fraction of the transcriptome. In addition to miRNAs, other bilaterian small RNAs, known as Piwi-interacting RNAs (piRNAs), protect the genome from transposons. Here we identify small RNAs from animal phyla that diverged before the emergence of the Bilateria. The cnidarian Nematostella vectensis (starlet sea anemone), a close ...[more]

PMID: 18830242

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The Early Origins and Evolution of microRNAs and piRNAs in Animals

Project description:We explored the potential for small RNA biology in organisms that diverged basal to Bilateria, identifying both miRNAs and piRNAs in Nematsotella and Amphimedon

2008-10-01 | GSE12578 | GEO

The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer (small RNA sequencing)

Project description:The Tasmanian devil, a marsupial carnivore, is endangered due to the emergence of a clonally transmissible cancer known as Devil Facial Tumor Disease (DFTD). This fatal cancer is clonally derived and is an allograft transmitted between devils by biting. We performed a large-scale genetic analysis of DFTD with microsatellite genotyping, mitochondrial genome analysis, as well as deep sequencing of the DFTD transcriptome and miRNAs. These studies confirm that DFTD is a monophyletic clonally transmissible tumor, and suggest that the disease is of Schwann cell origin. On the basis of these results we have generated a diagnostic marker for DFTD, and identify a suite of genes of relevance to DFTD pathology and transmission. We provide a genomic dataset for the Tasmanian devil, which is applicable to cancer diagnosis, disease evolution and conservation biology. This submission contains only small RNA sequence data from this study. Small RNA (18 - 24 nt) sequences from 15 Tasmanian devil (Sarcophilus harrisii) tissue samples

2010-01-01 | E-GEOD-18352 | biostudies-arrayexpress

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A high-resolution Amphimedon queenslandica transriptomic timecourse

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2014-01-24 | E-GEOD-54364 | biostudies-arrayexpress

Compatibility with Killer explains the Rise of RNAi-deficient Fungi

Project description:This SuperSeries is composed of the following subset Series: GSE31288: The impact of RNAi on the Saccharomyces cerevisiae transcriptome GSE31290: Small RNAs in S. cerevisiae reconstituted with RNAi Refer to individual Series

2011-08-09 | E-GEOD-31300 | biostudies-arrayexpress

Small RNAs generated in vitro by budding-yeast Dicer

Project description:The Dicer ribonuclease III (RNase III) enzymes process long double-stranded RNA (dsRNA) into the small interfering RNAs (siRNAs) that direct RNA interference. Here, we describe the structure and activity of a catalytically active fragment of Kluyveromyces polysporus Dcr1, which represents the noncanonical Dicers found in budding yeast. The crystal structure reveals a homodimer that resembles bacterial RNase III but includes a novel N-terminal domain and newly identified catalytic residues conserved throughout eukaryotic RNase III enzymes. Biochemical analyses show that Dcr1 dimers bind cooperatively along the dsRNA substrate and cleave at precise intervals based on the distance between consecutive active sites. Thus, unlike canonical Dicers, which successively remove siRNA duplexes from the dsRNA termini, Dcr1 initiates processing in the interior and works outward. The distinct mechanism of budding-yeast Dicers establishes a novel paradigm for natural protein-based molecular rulers and imparts substrate preferences with ramifications for biological function. High-throughput sequencing of small RNAs generated by in vitro processing of long dsRNA using Kluyveromyces polysporus Dicer

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2009-09-10 | E-GEOD-17870 | biostudies-arrayexpress

The impact of RNAi on the Saccharomyces cerevisiae transcriptome

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2011-08-10 | E-GEOD-31288 | biostudies-arrayexpress

Structure of yeast Argonaute with guide RNA

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2012-05-13 | E-GEOD-37725 | biostudies-arrayexpress

Natural variation in processability of individual Arabidopsis thaliana microRNAs

Project description:Like protein coding genes, loci that produce microRNAs (miRNAs) are generally considered to be under purifying selection, consistent with miRNA polymorphisms being able to cause disease. Nevertheless, it has been hypothesized that variation in miRNA genes may contribute to phenotypic diversity. Here we demonstrate that a naturally occurring polymorphism in the MIR164A gene interacts epistatically with an unlinked locus to affect leaf shape and shoot architecture in Arabidopsis thaliana. A single-base pair substitution in the miRNA complementary sequence alters the stability of the miRNA:miRNA* duplex. It thereby interferes with processing of the precursor and greatly reduces miRNA accumulation. We demonstrate that this is not a rare exception, but that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA processability due to cis mutations is a common contributor to phenotypic variation in plants. sRNA sequencing transgenic A. thaliana

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