The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Fischer, Sylvia E. J.; Montgomery, Taiowa A.; Zhang, Chi; Fahlgren, Noah; Breen, Peter C.; Hwang, Alexia; Sullivan, Christopher; Carrington, James C.; Ruvkun, Gary

doi:10.1371/journal.pgen.1002369

Cited by 79 publications

(160 citation statements)

References 51 publications

(112 reference statements)

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“…Analysis of endo-siRNA target suggested a difference between primary and secondary endo-siRNA targets as 18-to 22-mer siRNAs associated with genes required for embryonic development, 23-mers associated uniquely with post-embryonic development, and 24-26-mers associated with phosphorus metabolism or protein modification (Asikainen et al, 2008). It was also shown that in oocytes and embryos, ERGO-1-associated 26G siRNAs and NRDE-3-associated 22G siRNAs silence recently duplicated genes (Vasale et al, 2010;Fischer et al, 2011).…”

Section: Endogenous Rnai In the Germline And Somamentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFSA Supporting Publications

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This report is the outcome of an EFSA procurement aiming at investigating and summarising the state of knowledge on (I) the mode-of-action of dsRNA and miRNA pathways, (II) the potential for nontarget gene regulation by dsRNA-derived siRNAs or miRNAs, (III) the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing. The report is based on a comprehensive and systematic literature search, starting with the identification and retrieval of~190,000 publications related to the research area and further filtered down with keywords to produce focused collections used for subsequent screening of titles and abstracts. The report is comprised of an (I) Introduction to the field of small RNAs, (II) a Data and Methodologies section containing strategies used for literature search and study selection, and (III) the Results of the literature review organized according to the three main procurement tasks. The outcome of the first task reviews dsRNA and miRNA pathways in mammals (including humans), birds, fish, arthropods, annelids, molluscs, nematodes, and plants. Eight taxon-dedicated chapters are based on~1,400 cumulative references chosen from~10,000 inspected titles and abstracts. We review conserved and divergent aspects of small RNA pathways and dsRNA responses in animals and plants including structure and function of key proteins as well as four basic mechanisms: genome-encoded posttranscriptional regulations (miRNA), degradation of RNAs by short interfering RNA pools generated from long dsRNA (RNAi), transcriptional silencing, and sequence-independent responses to dsRNA. The outcome of the second task focuses on base pairing between small RNAs and their target RNAs and predictability of biological effects of small RNAs in animals and plants. The outcome of the last task reviews methodology, siRNA pools, and movement of small RNAs in plants. Potential transfer of small RNAs between species and circulating miRNAs in mammals is described in the final chapter.

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Section: Endogenous Rnai In the Germline And Somamentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFSA Supporting Publications

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“…One class is enriched in oocytes and embryos and associates with ERGO-1 (Han et al 2009;Vasale et al 2010;Fischer et al 2011). The other class associates with ALG-3 and ALG-4 during spermatogenesis (Han et al 2009;Conine et al 2010).…”

Section: Embryo and Sperm Class 26g Sirna Pathways Are Conserved In Cmentioning

confidence: 99%

“…From our C. elegans embryo small RNA library, we defined a set of 29 26G siRNA-yielding genes, which produced at least 10 26G siRNA reads per million total reads (RPM), 26 of which were previously annotated as ERGO-1 targets (Han et al 2009;Vasale et al 2010;Fischer et al 2011). In addition, we identified 121 embryo 26G siRNA-yielding genes in C. briggsae, 71 in C. remanei, and 272 in C. brenneri.…”

Section: Embryo and Sperm Class 26g Sirna Pathways Are Conserved In Cmentioning

confidence: 99%

“…In C. elegans, oocyte/embryo class 26G siRNAs tend to be generated from gene-poor arms of chromosomes ( Fig. 6D; Vasale et al 2010;Fischer et al 2011). In C. briggsae, for which the DNA sequence has been assembled on chromosomes, embryo class 26G siRNAs also tend to derive from chromosome arms (Fig.…”

Section: Org Downloaded Frommentioning

confidence: 99%

“…The 26G siRNAs fall into two classes: a spermatogenesisenriched class which associates with the AGO clade Argonautes, ALG-3 and ALG-4 (Han et al 2009;Conine et al 2010); and an oocyte-and embryo-enriched class which associates with the divergent PIWI-clade Argonaute, ERGO-1 (Han et al 2009;Vasale et al 2010;Fischer et al 2011). Both classes of 26G siRNAs are produced by the RdRP RRF-3 and are thought to trigger secondary 22G siRNA production.…”

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High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes

Shi

Montgomery

et al. 2013

Genome Res.

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The nematode Caenorhabditis elegans contains each of the broad classes of eukaryotic small RNAs, including microRNAs (miRNAs), endogenous small-interfering RNAs (endo-siRNAs), and piwi-interacting RNAs (piRNAs). To better understand the evolution of these regulatory RNAs, we deep-sequenced small RNAs from C. elegans and three closely related nematodes: C. briggsae, C. remanei, and C. brenneri. The results reveal a fluid landscape of small RNA pathways with essentially no conservation of individual sequences aside from a subset of miRNAs. We identified 54 miRNA families that are conserved in each of the four species, as well as numerous miRNAs that are species-specific or shared between only two or three species. Despite a lack of conservation of individual piRNAs and siRNAs, many of the features of each pathway are conserved between the different species. We show that the genomic distribution of 26G siRNAs and the tendency for piRNAs to cluster is conserved between C. briggsae and C. elegans. We also show that, in each species, 26G siRNAs trigger stage-specific secondary siRNA formation. piRNAs in each species also trigger secondary siRNA formation from targets containing up to three mismatches. Finally, we show that the production of male-and female-specific piRNAs is conserved in all four species, suggesting distinct roles for piRNAs in male and female germlines.

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Assays for Direct and Indirect Effects of C. elegans Endo-siRNAs

Shiu

Zhuang

Hunter

2014

Methods in Molecular Biology

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Summary Ever since the discovery of the first microRNAs in C. elegans, increasing numbers of endogenous small RNAs have been discovered. Endogenous siRNAs (endo-siRNAs) have emerged in the last few years as a largely independent class of small RNAs that regulate endogenous gene expression, with mechanisms distinct from those of piRNAs and miRNAs. Quantification of these small RNAs and their effect on target RNAs is a powerful tool for the analysis of RNAi; however, detection of small RNAs can be difficult due to their small size and relatively low abundance. Here, we describe the novel FirePlex assay for directly detecting endo-siRNA levels in bulk, as well as an optimized qPCR method for detecting the effect of endo-siRNAs on gene targets. Intriguingly, the loss of endo-siRNAs frequently results in enhanced experimental RNAi. Thus, we also present an optimized method to assess the indirect impact of endo-siRNAs on experimental RNAi efficiency.

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The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Cited by 79 publications

References 51 publications

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes

Assays for Direct and Indirect Effects of C. elegans Endo-siRNAs

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