Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons

Chung, Wei-Jen; Okamura, Katsutomo; Martı́n, Raquel; Lai, Eric C.

doi:10.1016/j.cub.2008.05.006

Cited by 265 publications

(303 citation statements)

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“…Deep sequence analysis of endogenous Drosophila siRNAs (endo siRNAs) from embryos, larval discs, and adult structures, as well as from S2 cells and Kc cells, indicates almost twenty percent of the endo siRNAs are derived from transposable elements in a Dcr-2-dependent process and represent both the sense (41%) and antisense strand (59%) of the transposon RNAs along the entire body of the transposable element, consistent with the formation of transposon dsRNA (11,12). In line with these observations, significant amounts of cytoplasmic, polyadenylated dsRNA, representing the entirety of the transposons mdg1 and mdg3, was identified in the Drosophila cell line 67J25D by the Georgiev laboratory nearly 30 years ago (13).…”

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confidence: 88%

“…We looked at the impact of D-elp1 depletion on transposon suppression and the production of the corresponding endo siRNA for representative transposons highly expressed in S2 cells. Previous studies have shown that a reduction in the RISC components Ago2 and Dcr-2, but not Dcr-1, result in the increased steady state levels of several transposon RNAs, including 297, mdg1, and the non-LTR transposon TART-B (11,12,32) accompanied by a decrease in the corresponding transposon endo-siRNAs. We measured the RNA levels for 297, mdg1, and the telomeric non-LTR transposon, HetA, after treating S2 cells with dsRNA to D-elp1, using Dcr-2 depletion as the positive control (32).…”

Section: D-elp1 Has a Role In Transposon Suppressionmentioning

confidence: 98%

“…The Drosophila genome harbors a variety of retrotransposons and mobile elements that are silenced post transcriptionally through the RNAi pathway (11,12,(29)(30)(31). We looked at the impact of D-elp1 depletion on transposon suppression and the production of the corresponding endo siRNA for representative transposons highly expressed in S2 cells.…”

Section: D-elp1 Has a Role In Transposon Suppressionmentioning

confidence: 99%

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RETRACTED: Identification of an RNA-dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression

Lipardi

Paterson

2009

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

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The authors wish to note the following: "In our article, we reported that recombinant subunit 1 of the Drosophila elongator complex, D-elp1, had RNA-dependent RNA polymerase (RdRP) activity and was involved in RNAi, transposon suppression, and endo-siRNA production, but not miRNA targeting. RdRP activity was identified using three assays to interrogate the reaction products: Dcr2 digestion, RNase sensitivity, and nearest neighbor analysis. Although we do see differential Dcr2 cleavage and RNase resistance, the gold standard for second strand RNA synthesis is nearest neighbor analysis, as described previously for the Neurospora crassa RdRP, QDE-1 (1). Subsequent studies revealed that the nearest neighbor analysis was misinterpreted because of two factors unknown to us at the time: First, T7 run-off transcripts used as single-stranded RNA templates have heterogeneous 3' termini (2, 3); Second, the Flag-tag affinity purified recombinant D-elp1 protein preparations used in our study contain a ribonucleotide terminal transferase activity able to catalyze the addition of single a-labeled ribonucleotide triphosphates to the 3' hydroxyl terminus of the template RNA. Therefore, nearest neighbor analysis measured the heterogeneous 3' termini of the template RNA and not second strand RNA synthesis, as initially reported. Given this result, we wish to rescind the interpretation that D-elp1 can be considered as an RNA-dependent RNA polymerase. The basis for the ribonucleotide terminal transferase activity is under investigation. The interpretation of the results does not detract from the fact that D-elp1 is involved in RNAi, endo-siRNA production, and transposon suppression, but not miRNA targeting as shown in Figs. 3 and 4. By clarifying this issue, we hope to promote further productive investigation into the role of elongator subunit 1 in RNAi and transposon suppression. We apologize for any difficulties our original interpretation may have caused other investigators and hereby retract the paper." Concetta Lipardi Bruce M. Paterson

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confidence: 88%

Section: D-elp1 Has a Role In Transposon Suppressionmentioning

confidence: 98%

Section: D-elp1 Has a Role In Transposon Suppressionmentioning

confidence: 99%

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RETRACTED: Identification of an RNA-dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression

Lipardi

Paterson

2009

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

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“…Moreover, the Ding laboratory showed that viral siRNAs generated during an acute infection also did not depend on AGO2 for their accumulation; in fact they observed overaccumulation of FHV-derived siRNAs after infection of ago2 mutants with attenuated FHV (5). The accumulation of unloaded viral siRNAs during acute and latent infections contrasts strongly with the behavior of diverse classes of endo-siRNAs, for which Northern analysis demonstrates them to require AGO2 for their stable accumulation (17,18,23,24,32).…”

Section: Discussionmentioning

confidence: 99%

“…The reads were clipped of the 3Ј linkers, and submitted to the National Center for Biotechnology Information Gene Expression Omnibus under the accessions GSM343832 and GSM343833 (S2R ϩ , first and second biological replicates) and GSM361908 (S2-GMR) cells. We also used data from an independent biological replicate of S2-GMR reads that we reported in GSM272652 (32).…”

Section: Methodsmentioning

confidence: 99%

Dicing of viral replication intermediates during silencing of latent Drosophila viruses

Flynt

Liu

Martı́n

et al. 2009

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

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103

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Previous studies revealed roles for RNA interference (RNAi) in the immediate cellular response to viral infection in plants, nematodes and flies. However, little is known about how RNAi combats viruses during persistent or latent infections. Our analysis of small RNAs cloned from Drosophila cells latently infected with Flock House Virus (FHV) failed to reveal signatures of bulk degradation of the viral genome. Instead, this ؉ strand virus specifically generated Dicer-2-dependent, 21-nucleotide siRNAs that derived in equal proportion from ؉ and ؊ strands. Curiously, luciferase reporters that are fully complementary to abundant viral siRNAs were poorly repressed. Moreover, although the viral siRNAs that were incorporated into an effector complex associated with Argonaute2, bulk FHV siRNAs in latently infected cells were not loaded into any Argonaute protein. Together, these data suggest that direct dicing of viral replication intermediates plays an important role in maintaining the latent viral state. In addition, the denial of bulk viral siRNAs from effector complexes suggests that criteria beyond the structural competency of RNA duplexes influence the assembly of functional silencing complexes.Argonaute2 ͉ Dicer-2 ͉ RNA interference ͉ virus G enetic analyses showed that core components of the RNA interference (RNAi) pathway generate viral small interfering RNAs (siRNAs) and restrict virus accumulation in flies (1-5), worms (6-8), and plants (9, 10). Such studies indicate that the cellular defense to viral infection begins when double-stranded RNA (dsRNA) viral genomes or replication intermediates are cleaved by Dicer-class RNase III enzymes into small interfering RNAs (siRNAs). The viral siRNAs are incorporated into Argonaute complexes that subsequently cleave and degrade viral coding RNAs, preventing completion of the viral lifecycle. To counteract the RNAi defense, many viruses have evolved proteins that inhibit various components of the RNAi pathway, thus permitting their successful replication and/or infection (11).In Drosophila, the RNAi and microRNA (miRNA) pathways are genetically distinct, but have substantial cross-talk (12). The canonical RNAi pathway uses Dicer-2 to process dsRNA into siRNAs, which are mostly loaded into Argonaute2 (AGO2) complex. AGO2-resident RNAs are then methylated at their 3Ј ends by the Hen1 methyltransferase (13,14). The miRNA pathway uses Dcr-1 to process premiRNA hairpins into mature miRNAs, which are mostly loaded into Argonaute1 (AGO1) complex; they remain unmethylated. Recent studies demonstrated that the sorting of diced small RNAs is influenced by the structural features of their duplex precursors. Small RNAs from perfectly double stranded duplexes are favored to enter AGO2, whereas central bulges favor entry into AGO1 (15, 16). However, these rules do not entirely explain the types of RNAs that are resident in AGO1 and AGO2 (17, 18); therefore, there are presumably additional determinants that affect small RNA loading.Because the studies to date focused on the role of R...

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RNA as a Regulator of Chromatin Structure

Murakami

2014

Encyclopedia of Molecular Cell Biology and Molecular Medicine

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Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons

Abstract: Drosophila utilizes two small-RNA systems to restrict transposon activity in the germline (mostly via piRNAs) and in the soma (mostly via siRNAs).

Cited by 265 publications

References 40 publications

RETRACTED: Identification of an RNA-dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression

RETRACTED: Identification of an RNA-dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression

Dicing of viral replication intermediates during silencing of latent Drosophila viruses

RNA as a Regulator of Chromatin Structure

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