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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Mutant analysis of C. elegans small RNAs, 5p-end-independent

ABSTRACT: These datasets profile the expression of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) in young adult worms from the wt and prg-1 mutant backgrounds. They were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as described in Ambros et al. (2003) Curr Biol 13:807-18. These datasets were prepared in the Craig C. Mello laboratory. Keywords: endo-siRNA mutant expression profiling CE-prg1-endoSiRNAs-Illumina 1 flowcell each for the wt and prg-1 mutant

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: James Ruby

PROVIDER: E-GEOD-11736 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans.

Batista Pedro J PJ Ruby J Graham JG Claycomb Julie M JM Chiang Rosaria R Fahlgren Noah N Kasschau Kristin D KD Chaves Daniel A DA Gu Weifeng W Vasale Jessica J JJ Duan Shenghua S Conte Darryl D Luo Shujun S Schroth Gary P GP Carrington James C JC Bartel David P DP Mello Craig C CC

Molecular cell 20080619 1

In metazoans, Piwi-related Argonaute proteins have been linked to germline maintenance, and to a class of germline-enriched small RNAs termed piRNAs. Here we show that an abundant class of 21 nucleotide small RNAs (21U-RNAs) are expressed in the C. elegans germline, interact with the C. elegans Piwi family member PRG-1, and depend on PRG-1 activity for their accumulation. The PRG-1 protein is expressed throughout development and localizes to nuage-like structures called P granules. Although 21U- ...[more]

PMID: 18571452

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Mutant analysis of C. elegans small RNAs with 5p monophosphates

Project description:These datasets profile the expression of small RNAs with 5p monophosphates and 3p hydroxyls (including miRNAs, 21U-RNAs) in young adult worms from the wt, prg-1 mutant, and fog-2 mutant backgrounds. These datasets were prepared in the Craig C. Mello laboratory using T4 RNA ligase 1. Keywords: miRNA and 21U-RNA discovery and mutant expression profiling CE-mutProfile-5pDependent-Illumina 1 flowcell each for the wt, prg-1 mutant, and fog-2 mutant

2008-06-15 | E-GEOD-11735 | biostudies-arrayexpress

C. elegans PRG-1 co-IP small RNAs, 5p-end-independent

Project description:These datasets examine the association of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) with the PRG-1 protein through co-immunoprecipitation. Two datasets are provided; one sequences small RNAs that co-IP with PRG-1; the other sequences small RNAs from the IP input sample. These RNA samples were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as described in Ambros et al. (2003) Curr Biol 13:807-18. These datasets were prepared in the Craig C. Mello laboratory. Keywords: identification of PRG-1-associated small RNAs

2008-06-16 | GSE11737 | GEO

Mutant analysis of C. elegans small RNAs, 5p-end-independent

Project description:These datasets profile the expression of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) in young adult worms from the wt and prg-1 mutant backgrounds. They were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as described in Ambros et al. (2003) Curr Biol 13:807-18. These datasets were prepared in the Craig C. Mello laboratory. Keywords: endo-siRNA mutant expression profiling

2008-06-16 | GSE11736 | GEO

Function, targets and evolution of Caenorhabditis elegans piRNAs (mRNA)

Project description:piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene, pseudogene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes but not pseudogenes or transposons. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNAi in C. elegans. Affymetrix mRNA expression data from wild-type and two independent prg-1;prg-2 double mutant C. elegans strains (mRNA)

2012-06-17 | E-GEOD-37432 | biostudies-arrayexpress

The expression of small RNAs after prg-1 mutation

Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated. Examination of small RNA expression in six different developmental stages (embryo, L1, L2, L3, L4, young adult) and mRNA expression in four stages (L1,L2,L3,L4) of C. elegans prg-1 mutant (wm161) .

2014-06-09 | E-GEOD-56272 | biostudies-arrayexpress

The expression mRNAs after prg-1 mutation

2014-06-09 | E-GEOD-56271 | biostudies-arrayexpress

Expression analysis of Caenorhabditis elegans Bristol N2 prg-1 and Bristol N2 prg-1; daf-2 double mutant

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2013-06-01 | E-GEOD-40569 | biostudies-arrayexpress

Maternal piRNAs are essential for germline development following de-novo establishment of endo-siRNAs in Caenorhabditis elegans

Project description:The Piwi-piRNA pathway represents a germline specific transposon-defense system. C. elegans Piwi, prg-1, is a non-essential gene and triggers a secondary RNAi response that depends on so-called mutator genes, endo-siRNAs (22G-RNAs) and at least one 22G-RNA-binding Argonaute protein, HRDE-1. Interestingly, through a poorly understood mechanism, silencing of PRG-1 targets can become PRG-1 independent. This state, also known as RNAe, is heritable and depends on mutator genes and HRDE-1. We studied how the transgenerational memory of RNAe and the piRNA pathway interact. We find that maternally provided PRG-1 is required for the de-novo establishment of 22G-RNA populations, especially those targeting transposons. Strikingly, attempts to re-establish 22G-RNAs in absence of both PRG-1 and RNAe memory result in severe germline proliferation defects. This is accompanied by a disturbed balance between gene-activating and -repressing 22G-RNA pathways. We propose a model in which CSR-1 prevents the loading of HRDE-1 and that both PRG-1 and HRDE-1 help to keep mutator activity focused on the proper targets.

2015-08-13 | GSE68988 | GEO

Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution

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2011-12-22 | E-GEOD-32880 | biostudies-arrayexpress

Transgenerational changes in small RNA profiles of C.elegans mutants lacking PRG-1

Project description:An attempt to identify small non-coding RNAs that change with increasing generations after becoming homozygous for the loss of PRG-1 Small non-coding RNA (18-30nt) was extracted from animals the indicated number of generations after homozygosity was established

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