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Analysis of transgene siRNAs and ARL-8-dependent siRNAs in Caenorhabditis elegans

ABSTRACT: We analyzed the C. elegans small RNA response to high copy transgene sequences expressed in the soma in a wild type and an eri-6/7 mutant background. We also analyzed small RNA defects in the arl-8(tm2472) mutant. Transgene siRNAs are 22 nt long, mostly antisense, and correspond to the promoter, coding regions, the 3'UTR and plamsid sequences present on the transgene. Transgene siRNAs are decreased in the eri-6/7 mutant. In the arl-8 mutant, 26G siRNAs in the ALG-3/4 dependent endogenous RNAi pathway are decreased. Sequencing small RNAs from C. elegans transgenic strains and mutants.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Sylvia Fischer

PROVIDER: E-GEOD-52785 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of transgene siRNAs and ARL-8-dependent siRNAs in Caenorhabditis elegans

Project description:We analyzed the C. elegans small RNA response to high copy transgene sequences expressed in the soma in a wild type and an eri-6/7 mutant background. We also analyzed small RNA defects in the arl-8(tm2472) mutant. Transgene siRNAs are 22 nt long, mostly antisense, and correspond to the promoter, coding regions, the 3'UTR and plamsid sequences present on the transgene. Transgene siRNAs are decreased in the eri-6/7 mutant. In the arl-8 mutant, 26G siRNAs in the ALG-3/4 dependent endogenous RNAi pathway are decreased.

2013-12-15 | GSE52785 | GEO

Gene expression profile of alg-3(tm1155);alg-4(ok1041) animals compared to wild type

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High throughput sequencing of endogenous small RNAs from AGO pathway mutants

Project description:High-throughput pyrosequencing of endogenous small RNAs from >95% male enriched populations of alg-3(tm1155);alg-4(ok1041);fog-2(q71) and fog-2(q71) worms as well as purified spermatids from fem-3(q20) adult worms. Gametogenesis is thermosensitive in numerous metazoa ranging from worms to man. In C. elegans a variety of germ-line nuage- (P-granule) -associated RNA-binding proteins including the Piwi-clade Argonaute, PRG-1, have been implicated in temperature-dependent fertility. Here, we describe the role of two AGO-class paralogs, alg-3 (T22B3.2) and alg-4 (ZK757.3) in promoting male fertility at elevated temperatures. A rescuing GFP::alg-3 transgene is localized in P-granules beginning at the late pachytene stage of male gametogenesis. alg-3/4 double mutants lack a subgroup of small RNAs, named 26G-RNAs, which target and appear to down-regulate numerous spermatogenesis-expressed mRNAs. These findings add to a growing number of AGO pathways required for temperature-dependent fertility in C. elegans and support a model in which AGOs and their small RNA co-factors function to promote robustness in gene-expression networks. 3 samples examined. Small RNAs from alg-3(tm1155);alg-4(ok1041);fog-2(q71) males and fog-2(q71) males. Small RNAs from spermatids isolated from ferm-3(q20) worms.

2010-02-24 | E-GEOD-18729 | biostudies-arrayexpress

High throughput sequencing of endogenous small RNAs from AGO pathway mutants

2010-02-24 | GSE18729 | GEO

Caenorhabditis elegans

Project description:Analysis of transgene siRNAs and ARL-8-dependent siRNAs in Caenorhabditis elegans

| PRJNA230012 | ENA

Effects of ADARs on small RNA processing pathways in C. elegans

Project description:Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine to inosine in double-stranded RNA (dsRNA). To evaluate effects of ADARs on small RNAs that derive from dsRNA precursors, we performed deep-sequencing, comparing small RNAs from wildtype and ADAR mutant C. elegans. While editing in small RNAs was rare, at least 40% of microRNAs had altered levels in at least one ADAR mutant strain, and miRNAs with significantly altered levels had mRNA targets with correspondingly affected levels. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also had altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. The 26G class of endo-siRNAs was significantly affected by ADARs, and many altered 26G loci had intronic reads, and histone modifications associated with transcriptional silencing. Our data indicate ADARs, through both direct and indirect mechanisms, are important for maintaining wildtype levels of many small RNAs in C. elegans.

2012-04-05 | GSE28888 | GEO

ADARs affect the biogenesis of many small RNAs in C. elegans, but few mature small RNAs are edited

2012-04-04 | E-GEOD-28888 | biostudies-arrayexpress

Endo-siRNAs in C. elegans spermatogenesis and their requirement for the RdRP RRF-3

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2010-01-13 | E-GEOD-18429 | biostudies-arrayexpress

The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications.

Project description:To characterize the role of the ERI-6/7 helicase in endogenous small RNA pathways in C. elegans, small RNA populations from null alleles of eri-6 and eri-7, and from mutants of known endogenous RNAi pathway factors, eri-1 and ergo-1, were determined by deep sequencing, and compared to wild type. Small RNA analysis in wild type and eri-1, ergo-1, eri-6 and eri-7 mutant C. elegans strains.

2011-09-25 | E-GEOD-32366 | biostudies-arrayexpress

Whole genome microarray analysis of C. elegans rrf-3 and eri-1 mutants

Project description:RRF-3 and ERI-1 are first identified proteins required for accumulation of at least some endogenous secondary siRNAs in C.elegans. Genome wide gene expression analysis was performed on L4 stage rrf-3 and eri-1 mutant C. elegans to study effects caused by loss of these proteins. Mutant rrf-3 and eri-1 strains exhibited similar expression patterns when compared to N2 wild type, while 72 transcripts were found to be co-overexpressed and 4 transcripts co-underexpressed (> 2-fold, p< 0.05). Ontology analysis indicated many of the gene products were associated with protein phosphorylation and sperm function. These results provide additional support for the hypothesis that RRF-3 and ERI-1 act together in a siRNA pathway and may indicate biological processes that are related to endo-siRNAs. Keywords: Mutant vs. wild type -comparison

2007-10-19 | GSE8659 | GEO

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