In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans

Aoki, Kai; Moriguchi, Hiromi; Yoshioka, Tomoko; Okawa, Katsuya; Tabara, Hiroaki

doi:10.1038/sj.emboj.7601910

Cited by 204 publications

(278 citation statements)

References 37 publications

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“…CSR-1 is an Argonaute protein with endonucleolytic mRNA cleavage (slicing) activity (Yigit et al 2006;Aoki et al 2007). The slicing activity of Argonautes mediates siRNA silencing of mRNAs, which are then degraded by exonucleases in the exosome and decapping pathways (Orban and Izaurralde 2005).…”

Section: Resultsmentioning

confidence: 99%

“…Many of these components fall into specific gene classes with shared P-granule phenotypes, allowing us to better understand how cellular processes converge on Pgranule assembly and function. We looked closely at the striking phenotype, accumulation of enlarged P granules, caused by RNAi depletion of CSR-1, an Argonaute that was previously shown to target its mRNA slicing activity through secondary siRNAs (Yigit et al 2006;Aoki et al 2007). Loss of other predicted members of a secondary siRNA pathway, the RNA-dependent RNA polymerase EGO-1 and the DExH helicase DRH-3, causes a similar phenotype.…”

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confidence: 99%

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A Genomewide RNAi Screen for Genes That Affect the Stability, Distribution and Function of P Granules in Caenorhabditis elegans

2009

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P granules are non-membrane-bound organelles found in the germ-line cytoplasm throughout Caenorhabditis elegans development. Like their ''germ granule'' counterparts in other animals, P granules are thought to act as determinants of the identity and special properties of germ cells, properties that include the unique ability to give rise to all tissues of future generations of an organism. Therefore, understanding how P granules work is critical to understanding how cellular immortality and totipotency are retained, gained, and lost. Here we report on a genomewide RNAi screen in C. elegans, which identified 173 genes that affect the stability, localization, and function of P granules. Many of these genes fall into specific classes with shared P-granule phenotypes, allowing us to better understand how cellular processes such as protein degradation, translation, splicing, nuclear transport, and mRNA homeostasis converge on P-granule assembly and function. One of the more striking phenotypes is caused by the depletion of CSR-1, an Argonaute associated with an endogenous siRNA pathway that functions in the germ line. We show that CSR-1 and two other endo-siRNA pathway members, the RNA-dependent RNA polymerase EGO-1 and the helicase DRH-3, act to antagonize RNA and P-granule accumulation in the germ line. Our findings strengthen the emerging view that germ granules are involved in numerous aspects of RNA metabolism, including an endo-siRNA pathway in germ cells.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

A Genomewide RNAi Screen for Genes That Affect the Stability, Distribution and Function of P Granules in Caenorhabditis elegans

2009

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“…By using the target RNA as a template, RNA-dependent RNA polymerases catalyze the biogenesis of secondary small RNAs [83]. siRNAs and piRNAs trigger such amplification, a process that generates a secondary RNAi response that persists long after the original RNA transcript is degraded [84][85][86][87].…”

Section: Mechanisms That Enable Long-lasting Rnaimentioning

confidence: 99%

Guest list or black list: heritable small RNAs as immunogenic memories

Rechavi

2014

Trends in Cell Biology

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Small RNA-mediated gene silencing plays a pivotal role in genome immunity by recognizing and eliminating viruses and transposons which otherwise may colonize the genome. However, this can be challenging since individual genomic parasites are highly diverse, and employ multiple immune evasion techniques. In this review, I discuss a new theory proposing that the integrity of the germline is maintained by transgenerationally-transmitted RNA "memories" that record ancestral gene expression patterns, and delineate "Self" from "Foreign" sequences. To maintain such recollection two tactics are employed in parallel: "black listing" of invading nucleic acids, and "guest listing" of endogenous genes. Studies in a number of organisms have shown that this memorization is used by the next generation small RNAs to act as "Inherited Vaccines" that ambush invading elements, or as "Inherited Licenses" that grant the transcription of autogenous sequences. KeywordsSmall RNA; Transgenerational Inheritance; Inherited Immunity; Self Vs. Non-Self; "Inherited Vaccines" Overview of transgenerational inheritanceEvolution progresses through an interplay between two major forces, selection and variation. Since the formulation of the Modern Synthesis the theory holds that the environment is limited in its contribution to the evolutionary course of action -it affects selection, but not the degree of variation [1,2]. However, recent discoveries in epigenetics suggest that the environment may influence variability as well [1]. If the parental environment is predictive of the conditions that the progeny will face (often for sessile or short-lived organisms), epigenetic responses can change the output of the encoded genetic information in an adaptive manner [3]. For example, the water flea Daphnia changes its normal developmental course and develops a "helmet" that protects it from predators, if it is born to a mother that survived a similar attack [4].Correspondence to: odedrechavi@gmail.com. Over the years, controversy surrounded the study of environmentally affected transgenerational inheritance. Today, an improved understanding of epigenetic mechanisms at the molecular level has provided a logical background to explain how, heretically, an adaptive acquired trait could become heritable [5]. Several epigenetic mechanisms could regulate the expression of relevant genes during transgenerational inheritance including DNA methylation, histone modification, and transmission of regulatory RNAs. Moreover, in many organisms, these pathways appear to be interconnected [5][6][7][8]. Europe PMC Funders GroupThis review will concentrate on recent discoveries that establish a role for small RNAs in transgenerational transmission of acquired defense. Furthermore, exciting examples of RNA-mediated non-Mendelian genetic effects will be discussed, along with their possible implications for the study of evolution and immunology. RNA-mediated gene silencing and inheritanceSince the original discovery that small RNAs derived from exogenously-provided dou...

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“…Secondary siRNAs promote the major effects on silencing of mRNAs but also, likely, on transcriptional silencing and heterochromatin formation [48]. Primary and secondary siRNAs have been demonstrated in C. elegans, having different modifications at the 5′ends [49,50].…”

Section: Small Rna -Mediators Of Rnaimentioning

confidence: 99%

“…The amplification model, suggested by Yigit et al [47,48], makes a distinction between rare primary siRNA "triggers", products of Dicer processing of double stranded precursors, and abundant secondary siRNAs, synthesized by RNA dependent polymerases (RDPs). Secondary siRNAs promote the major effects on silencing of mRNAs but also, likely, on transcriptional silencing and heterochromatin formation [48].…”

Section: Small Rna -Mediators Of Rnaimentioning

confidence: 99%

Epigenetics: heterochromatin meets RNAi

2009

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The term epigenetics refers to heritable changes not encoded by DNA. The organization of DNA into chromatin fibers affects gene expression in a heritable manner and is therefore one mechanism of epigenetic inheritance. Large parts of eukaryotic genomes consist of constitutively highly condensed heterochromatin, important for maintaining genome integrity but also for silencing of genes within. Small RNA, together with factors typically associated with RNA interference (RNAi) targets homologous DNA sequences and recruits factors that modify the chromatin, commonly resulting in formation of heterochromatin and silencing of target genes. The scope of this review is to provide an overview of the roles of small RNA and the RNAi components, Dicer, Argonaute and RNA dependent polymerases in epigenetic inheritance via heterochromatin formation, exemplified with pathways from unicellular eukaryotes, plants and animals.

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In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans

Cited by 204 publications

References 37 publications

A Genomewide RNAi Screen for Genes That Affect the Stability, Distribution and Function of P Granules in Caenorhabditis elegans

A Genomewide RNAi Screen for Genes That Affect the Stability, Distribution and Function of P Granules in Caenorhabditis elegans

Guest list or black list: heritable small RNAs as immunogenic memories

Epigenetics: heterochromatin meets RNAi

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