Analysis of 22G siRNA triggered siRNA amplification in Caenorhabditis elegans
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ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE34320 | GEO | 2011/12/10
SECONDARY ACCESSION(S): PRJNA156415
REPOSITORIES: GEO
Similar Datasets
Project description:To determine if an endogenous 22G siRNA sensor transgene is subject to siRNA amplification, small RNAs were deep sequenced from the sensor and from a control transgene that is identical to the sensor but lacks an siRNA target site. Small RNAs were isolated from synchronized young adult C. elegans and subjected to deep sequencing.
2011-12-10 | E-GEOD-34320 | biostudies-arrayexpress
Project description:Small RNAs, including piRNAs, miRNAs and endogenous siRNAs, bind Argonaute proteins to form RNA-silencing complexes that target coding genes, transposons and aberrant RNAs. To assess the requirements for endogenous siRNA formation and activity in C. elegans, we developed a GFP-based sensor for the endogenous siRNA 22G siR-1, one of a set of abundant siRNAs processed from a precursor RNA mapping to the X chromosome, the X-cluster. Silencing of the sensor is also dependent on the partially complementary, unlinked 26G siR-O7 siRNA. We show that 26G siR-O7 acts in trans to initiate 22G siRNA formation from the X-cluster. The presence of several mispairs between 26G siR-O7 and the X-cluster mRNA, as well as mutagenesis of the siRNA sensor, indicates that siRNA target recognition is permissive to a degree of mispairing. From a candidate reverse genetic screen, we identified several factors required for 22G siR-1 activity, including the Argonaute ergo-1 and the 3' methyltransferase henn-1. Quantitative RT-PCR of small RNAs in a henn-1 mutant and deep sequencing of methylated small RNAs indicate that siRNAs and piRNAs that associate with PIWI clade Argonautes are methylated by HENN-1, while siRNAs and miRNAs that associate with non-PIWI clade Argonautes are not. Thus, PIWI-class Argonaute proteins are specifically adapted to associate with methylated small RNAs in C. elegans. This SuperSeries is composed of the following subset Series: GSE34320: Analysis of 22G siRNA triggered siRNA amplification in Caenorhabditis elegans GSE34321: Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans Refer to individual Series
2012-02-03 | E-GEOD-35550 | biostudies-arrayexpress
Project description:Small RNAs, including piRNAs, miRNAs and endogenous siRNAs, bind Argonaute proteins to form RNA-silencing complexes that target coding genes, transposons and aberrant RNAs. To assess the requirements for endogenous siRNA formation and activity in C. elegans, we developed a GFP-based sensor for the endogenous siRNA 22G siR-1, one of a set of abundant siRNAs processed from a precursor RNA mapping to the X chromosome, the X-cluster. Silencing of the sensor is also dependent on the partially complementary, unlinked 26G siR-O7 siRNA. We show that 26G siR-O7 acts in trans to initiate 22G siRNA formation from the X-cluster. The presence of several mispairs between 26G siR-O7 and the X-cluster mRNA, as well as mutagenesis of the siRNA sensor, indicates that siRNA target recognition is permissive to a degree of mispairing. From a candidate reverse genetic screen, we identified several factors required for 22G siR-1 activity, including the Argonaute ergo-1 and the 3' methyltransferase henn-1. Quantitative RT-PCR of small RNAs in a henn-1 mutant and deep sequencing of methylated small RNAs indicate that siRNAs and piRNAs that associate with PIWI clade Argonautes are methylated by HENN-1, while siRNAs and miRNAs that associate with non-PIWI clade Argonautes are not. Thus, PIWI-class Argonaute proteins are specifically adapted to associate with methylated small RNAs in C. elegans. This SuperSeries is composed of the SubSeries listed below.
2012-02-03 | GSE35550 | GEO
Project description:Analysis of 22G siRNA triggered siRNA amplification in Caenorhabditis elegans
| PRJNA156415 | ENA
Project description:ERI-6/7 is a negative regulator of exogenous RNAi, however the function of SOSI-1 has never previously been characterized. We noticed that expression of sosi-1 and eri-6/7 are mutually exclusive. Due to its genomic locus being nested within the eri-6 locus, we hypothesized that sosi-1 could be acting as a regulator of ERI-6/7 function by disrupting eri-6/7 expression upon sensing changes in the production of MUT-16-dependent 22G siRNAs. Our data confirms that expression of the sosi-1 mRNA is regulated by MUT-16-dependent 22G siRNAs. In addition, we show here that the expression of the eri-6 and eri-7 pre-mRNAs, and thus the eri-6/7 trans-spliced mRNA, are mis-regulated upon loss of sosi-1-targeting and eri-6[e-f]-targeting MUT-16-dependent 22G siRNAs, suggesting that sosi-1 and eri-6[e-f] act as a feedback sensor for small RNA function.
2020-05-21 | GSE145217 | GEO
Project description:Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements in animals. In C. elegans, mutator-class (mut) genes mediate siRNA-guided repression of transposons as well as exogenous RNA-directed gene silencing (RNAi), but their roles in endogenous RNA silencing pathways are not well understood. To characterize the endogenous small RNAs dependent on mutator-class genes, small RNA populations from a null allele of mut-16, as well as a regulatory mut-16(mg461) allele that disables only somatic RNAi, were subjected to deep sequencing.
2011-02-01 | GSE26165 | GEO
Project description:To explore how ZSP-1 (and therefore Z granules) might contribute to germline RNAi, we asked if zsp-1(-) animals were able to produce 22G siRNAs in response to dsRNA exposure. We exposed wild-type and zsp-1(-) animals to dsRNA targeting the germline-expressed gene oma-1 and sequenced the resultant oma-1 22G siRNAs. We identified similar numbers of oma-1 siRNAs anti-sense to oma-1 after oma-1 RNAi on wild-type or zsp-1(-) animals. We also used this dataset to identify genes with differential level of targeted 22G siRNAs level in zsp-1(-) versus WT animals.
2020-05-21 | GSE150960 | GEO
Project description:Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements in animals. In Caenorhabditis elegans, mutator (mut) class genes mediate siRNA-guided repression of transposons as well as exogenous RNAi, but their roles in endogenous RNA silencing pathways are not well-understood. To characterize the endogenous small RNAs dependent on mut class genes, small RNA populations from a null allele of mut-16 as well as a regulatory mut-16(mg461) allele that disables only somatic RNAi were subjected to deep sequencing. Additionally, each of the mut class genes was tested for a requirement in 26G siRNA pathways. The results indicate that mut-16 is an essential factor in multiple endogenous germline and somatic siRNA pathways involving several distinct Argonautes and RNA-dependent RNA polymerases. The results also reveal essential roles for mut-2 and mut-7 in the ERGO-1 class 26G siRNA pathway and less critical roles for mut-8, mut-14, and mut-15. We show that transposons are hypersusceptible to mut-16-dependent silencing and identify a requirement for the siRNA machinery in piRNA biogenesis from Tc1 transposons. We also show that the soma-specific mut-16(mg461) mutant allele is present in multiple C. elegans laboratory strains.
| S-EPMC3029761 | biostudies-literature
Project description:Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements in animals. In C. elegans, mutator-class (mut) genes mediate siRNA-guided repression of transposons as well as exogenous RNA-directed gene silencing (RNAi), but their roles in endogenous RNA silencing pathways are not well understood. To characterize the endogenous small RNAs dependent on mutator-class genes, small RNA populations from a null allele of mut-16, as well as a regulatory mut-16(mg461) allele that disables only somatic RNAi, were subjected to deep sequencing. Small RNA analysis in wild type and mut-16 mutant C. elegans strains
2011-02-01 | E-GEOD-26165 | biostudies-arrayexpress
Project description:mut-16 and other mutator-class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans
| PRJNA135287 | ENA