Argonautes confront new small RNAs

Faehnle, C.R.; Joshua‐Tor, Leemor

doi:10.1016/j.cbpa.2007.08.032

Cited by 90 publications

(71 citation statements)

References 59 publications

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“…Argonaute proteins can be divided into three distinct groups (reviewed in Faehnle and Joshua-Tor, 2007): (1) AGO proteins, found in all kingdoms, (2) PIWI proteins found in animals, and (3) WAGO proteins found only in nematodes. The WAGO subfamily was described last, so it is not recognized in the older literature, which typically divides Argonaute proteins into AGO and PIWI subgroups (e.g.…”

Section: Dicer -Structure and Functionmentioning

confidence: 99%

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

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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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: Dicer -Structure and Functionmentioning

confidence: 99%

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

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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“…Argonaute proteins are central components of RISC and possess two conserved domains, PAZ and PIWI. Argonautes directly bind small RNAs (via both domains) and may possess target cleavage (''slicer'') activity via the PIWI domain (32). C. elegans encodes 27 potential Argonautes with diverse functions, several of which have been found to be enriched during spermatogenesis or oogenesis (27,33).…”

Section: Two Subclasses Of 26g Rnas Exhibit Different Expression Pattmentioning

confidence: 99%

26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans

Han

Manoharan

Harkins

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

172

301

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Endogenous small interfering RNAs (endo-siRNAs) regulate diverse gene expression programs in eukaryotes by either binding and cleaving mRNA targets or mediating heterochromatin formation; however, the mechanisms of endo-siRNA biogenesis, sorting, and target regulation remain poorly understood. Here we report the identification and function of a specific class of germline-generated endo-siRNAs in Caenorhabditis elegans that are 26 nt in length and contain a guanine at the first nucleotide position (i.e., 26G RNAs). 26G RNAs regulate gene expression during spermatogenesis and zygotic development, and their biogenesis requires the ERI-1 exonuclease and the RRF-3 RNA-dependent RNA polymerase (RdRP). Remarkably, we identified two nonoverlapping subclasses of 26G RNAs that sort into specific RNA-induced silencing complexes (RISCs) and differentially regulate distinct mRNA targets. Class I 26G RNAs target genes are expressed during spermatogenesis, whereas class II 26G RNAs are maternally inherited and silence gene expression during zygotic development. These findings implicate a class of endo-siRNAs in the global regulation of transcriptional programs required for fertility and development.endogenous siRNA ͉ germline ͉ RNA interference S mall RNAs bind Argonaute/Piwi proteins in the RNAinduced silencing complex (RISC) and, through base pairing, guide RISC to silence their cognate targets. While the taxonomy of small RNAs remains fluid, they can be defined in part by nucleotide length, 5Ј nucleotide composition, chemical modifications, genetic requirements for biogenesis, mode of silencing, and biological functions. For example, microRNAs are processed from double-stranded hairpin precursors by the RNase III-like enzyme Dicer to the Ϸ22-nt mature form containing a 5Ј-monophosphate nucleotide. The microRNAs associate with Argonaute (Ago) proteins in RISC and mediate translational repression and/or degradation of their target mRNAs (1). In contrast, Piwi-interacting RNAs (piRNAs) are typically longer than microRNAs, possess a uridine in the first nucleotide, and are generated by a Dicer-independent self-amplification pathway. The piRNAs bind to Piwi proteins in RISC and silence transposons (2).Endogenous small interfering RNAs (endo-siRNAs) represent an emerging class of small RNAs described and characterized in Caenorhabditis elegans by Ambros et al. (3). These endo-siRNAs are perfectly antisense to target transcripts and require the C. elegans Dicer, DCR-1, the RNA-dependent RNA polymerase (RdRP) RRF-3, and the exonuclease ERI-1 for expression (4,5). By large-scale pyrosequencing, Ruby et al. determined that other endo-siRNAs target transcripts associated with spermatogenesis and transposons (6). Therefore, C. elegans endo-siRNAs appear to be a diverse class of small RNAs, with distinct biological functions and genetic requirements for biogenesis. The recent discovery of endo-siRNAs derived from transposable elements, natural antisense transcripts, and hairpin RNAs in Drosophila melanogaster and Mus musculus (7-12) fur...

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“…piRNAs comprise the biggest and most complex class of small non-coding RNAs, and they are defined by their association with PIWI subclade members of AGO (Table 1). Argonautes, which are well-known key proteins in small RNA-mediated silencing complexes, are divided into AGO and PIWI subclades (Faehnle & Joshua-Tor 2007). AGOs are involved in RNA interference and in miRNA-mediated gene silencing and are ubiquitously expressed, while PIWIs are directly associated with piRNAs.…”

Section: ′ 5′mentioning

confidence: 99%

Chromatoid body and small RNAs in male germ cells

Meikar¹,

Ros²,

Korhonen³

et al. 2011

Reproduction

143

154

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The chromatoid body (CB) is a germ granule in the cytoplasm of postmeiotic haploid round spermatids that is loaded with RNA and RNAbinding proteins. Following the discovery of small non-coding RNA-mediated gene regulation and the identification of PIWI-interacting RNAs (piRNAs) that have crucial roles in germ line development, the function of the CB has slowly begun to be revealed. Male germ cells utilise small RNAs to control the complex and specialised process of sperm production. Several microRNAs have been identified during spermatogenesis. In addition, a high number of piRNAs are present both in embryonic and postnatal male germ cells, with their expression being impressively induced in late meiotic cells and haploid round spermatids. At postmeiotic stage of germ cell differentiation, the CB accumulates piRNAs and proteins of piRNA machinery, as well as several other proteins involved in distinct RNA regulation pathways. All existing evidence suggests a role for the CB in mRNA regulation and small RNA-mediated gene control, but the mechanisms remain uncharacterised. In this review, we summarise the current knowledge of the CB and its association with small RNA pathways.

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Argonautes confront new small RNAs

Cited by 90 publications

References 59 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

26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans

Chromatoid body and small RNAs in male germ cells

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