Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline

Gu, Weifeng; Shirayama, Masaki; Conte, Darryl; Vasale, Jessica J.; Batista, Pedro J.; Claycomb, Julie M.; Moresco, James J.; Youngman, Elaine M.; Keys, Jennifer A.; Stoltz, Matthew; Chen, Chun-Cheih G.; Chaves, Daniel A.; Duan, Shenghua; Kasschau, Krisitin D.; Fahlgren, Noah; Yates, John R.; Mitani, Shohei; Carrington, James C.; Mello, Craig C.

doi:10.1016/j.molcel.2009.09.020

Cited by 454 publications

(898 citation statements)

References 66 publications

Supporting

Mentioning

859

Contrasting

Order By: Relevance

“…Genome Research 503 www.genome.org siRNA amplification, are more abundant than CSR-1 class siRNAs in C. elegans Gu et al 2009;Phillips et al 2012). We observed that WAGO target genes, on average, produce higher levels of 22G siRNAs than CSR-1 target genes, regardless of whether or not the genes are conserved.…”

Section: Evolution Of Small Rna Pathways In Nematodesmentioning

confidence: 71%

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

Shi

Montgomery

et al. 2013

Genome Res.

View full text Add to dashboard Cite

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.

show abstract

Section: Evolution Of Small Rna Pathways In Nematodesmentioning

confidence: 71%

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

Shi

Montgomery

et al. 2013

Genome Res.

View full text Add to dashboard Cite

show abstract

“…We investigated FHV replication and Orsay virus infection in worms containing the ne4253 allele of drh-3. A single amino acid change occurred in the helicase C domain of DRH-3 encoded by the ne4253 allele, and as a result, worms containing this allele are defective in dsRNAinduced RNAi in the somatic tissues (25). We found that drh-3 mutant worms were highly susceptible to Orsay virus infection (Fig.…”

Section: The Helicase and Ctd Domains Of Rig-i Were Functional In A Fmentioning

confidence: 76%

“…S6). Recent studies have shown that DRH-3 is required for germline development and RNAi by participating in the biogenesis of 22G RNAs (25,38,39), suggesting a possible role for DRH-3 in antiviral RNAi. We investigated FHV replication and Orsay virus infection in worms containing the ne4253 allele of drh-3.…”

Section: The Helicase and Ctd Domains Of Rig-i Were Functional In A Fmentioning

confidence: 99%

“…These include Dicer-1 and dsRNA-binding protein RDE-4 (RNA interference-deficient 4), involved in the biogenesis of primary siRNAs predominantly 23 nt in length, and Argonaute protein RDE-1 (RNA interference-deficient 1) and RNA-dependent RNA polymerase RRF-1, required for the production of secondary siRNAs (18)(19)(20)(21)(22). Worm secondary siRNAs are 22-nt singlestranded RNAs with G as the 5′-terminal nt and antisense to the target mRNA, and are often referred as 22G RNAs (23)(24)(25). Intriguingly, antiviral RNAi in C. elegans is also regulated by Dicer-related RNA helicase 1 (DRH-1), which is highly homologous to mammalian RIG-I and is largely dispensable for exogenous RNAi (15).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Homologous RIG-I–like helicase proteins direct RNAi-mediated antiviral immunity in C. elegans by distinct mechanisms

Guo

Zhang

Wang

et al. 2013

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

123

View full text Add to dashboard Cite

RNAi-mediated antiviral immunity in Caenorhabditis elegans requires Dicer-related helicase 1 (DRH-1), which encodes the helicase and C-terminal domains homologous to the mammalian retinoic acid inducible gene I (RIG-I)-like helicase (RLH) family of cytosolic immune receptors. Here we show that the antiviral function of DRH-1 requires the RIG-I homologous domains as well as its wormspecific N-terminal domain. We also demonstrate that the helicase and C-terminal domains encoded by either worm DRH-2 or human RIG-I can functionally replace the corresponding domains of DRH-1 to mediate antiviral RNAi in C. elegans. Notably, substitutions in a three-residue motif of the C-terminal regulatory domain of RIG-I that physically interacts with viral double-stranded RNA abolish the antiviral activity of C-terminal regulatory domains of both RIG-I and DRH-1 in C. elegans. Genetic analysis revealed an essential role for both DRH-1 and DRH-3 in C. elegans antiviral RNAi targeting a natural viral pathogen. However, Northern blot and small RNA deep sequencing analyses indicate that DRH-1 acts to enhance production of viral primary siRNAs, whereas DRH-3 regulates antiviral RNAi by participating in the biogenesis of secondary siRNAs after Dicer-dependent production of primary siRNAs. We propose that DRH-1 facilitates the acquisition of viral double-stranded RNA by the worm dicing complex for the subsequent processing into primary siRNAs. The strong parallel for the antiviral function of RLHs in worms and mammals suggests that detection of viral doublestranded RNA may activate completely unrelated effector mechanisms or, alternatively, that the mammalian RLHs have a conserved activity to stimulate production of viral siRNAs for antiviral immunity by an RNAi effector mechanism.I nnate immunity refers to ancient host defense systems that act immediately after pathogen attack and are under the control of germline-encoded immune receptors. Pathogen sensing by several classes of immune receptors such as retinoic acid inducible gene I (RIG-I)-like cytosolic sensors in mammals leads to the transcriptional activation of effector genes in the nucleus (1). In contrast, detection of viral double-stranded RNA (dsRNA) by Dicer endonucleases is associated with the production of small interfering RNAs (siRNAs), which subsequently direct sequencespecific antiviral immunity through RNA interference (RNAi) (2-5). Antiviral RNAi is a major antiviral defense mechanism in fungi, plants, insects, and nematodes, so that suppression of the defense by a virus-encoded suppressor of RNAi is essential to establish infection (6-8). Although the RNAi machinery is highly conserved in mammals, conclusive evidence for a natural antiviral role of RNAi in mammals is not available (9).The nematode Caenorhabditis elegans has recently emerged as a small-animal model for innate immunity studies (10, 11). Genetic studies indicate that antiviral RNAi in C. elegans requires the genes essential for RNAi induced by exogenous dsRNA (12-17). These include Dicer-1 and dsRNA-bind...

show abstract

“…Several different systems involving small RNAs have evolved in eukaryotes for transposon control (3). In many cases, a system involving an RNA-dependent RNA polymerase (RDRP) amplification and Dicer processing of precursor transcripts is used (4,5). This endogenous small RNA defense mechanism shares many features with the RNAi mechanism first described in Caenorhabditis elegans (6).…”

mentioning

confidence: 99%

Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line

Wang

Elgin

2011

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

209

229

View full text Add to dashboard Cite

Transposon control is a critical process during reproduction. The PIWI family proteins can play a key role, using a piRNA-mediated slicing mechanism to suppress transposon activity posttranscriptionally. In Drosophila melanogaster , Piwi is predominantly localized in the nucleus and has been implicated in heterochromatin formation. Here, we use female germ-line–specific depletion to study Piwi function. This depletion of Piwi leads to infertility and to axis specification defects in the developing egg chambers; correspondingly, widespread loss of transposon silencing is observed. Germ-line Piwi does not appear to be required for piRNA production. Instead, Piwi requires Aubergine (and presumably secondary piRNA) for proper localization. A subset of transposons that show significant overexpression in germ-line Piwi-depleted ovaries exhibit a corresponding loss of HP1a and H3K9me2. Germ-line HP1a depletion also leads to a loss of transposon silencing, demonstrating the functional requirement for HP1a enrichment at these loci. Considering our results and those of others, we infer that germ-line Piwi functions downstream of piRNA production to promote silencing of some transposons via recruitment of HP1a. Thus, in addition to its better-known function in posttranscriptional silencing, piRNA also appears to function in a targeting mechanism for heterochromatin formation mediated by Piwi.

show abstract

Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline

Cited by 454 publications

References 66 publications

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

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

Homologous RIG-I–like helicase proteins direct RNAi-mediated antiviral immunity in C. elegans by distinct mechanisms

Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line

Contact Info

Product

Resources

About