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

Abstract

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

The role of small non-coding RNAs in genome stability and chromatin organization

“…In some organisms, this results in the formation of new dsRNA, which is processed by Dicer into secondary siRNAs; in other organisms, Dicer is not involved in the amplification step and the RdRP is thought to synthesize single-stranded secondary siRNAs directly. Although only a subset of eukaryotes (including Schizosaccharomyces pombe, Neurospora, Caenorhabditis elegans and plants) encode an obvious RdRP enzyme in their genomes, several other animal species were recently found to posses RdRP activity mediated by divergent enzyme complexes (Lipardi and Paterson, 2009;Maida et al, 2009). This suggests that amplification of siRNAs is potentially more widely conserved than the conservation of the RdRP enzyme suggests.…”

Effective Gene Silencing in a Microsporidian Parasite Associated with Honeybee ( Apis mellifera ) Colony Declines

“…Apparently, these SID1-like proteins channel double-stranded RNAs (dsRNAs) between cells, enabling systemic spread of the silencing signal (1). Although a canonical invertebrate RNA-dependent RNA polymerase (RdRP) homologue has not yet been described, there is evidence that such RdRP activity may occur via other enzymes, leading to amplification of the silencing signal in insects (26).…”

Antiviral responses of arthropod vectors: an update on recent advances

“…In D. melanogaster it has been shown that systemic spread of the RNAi response is essential for an efficient antiviral response and components of the dsRNA uptake machinery have been identified [60,98]. To date no protein with RNA-dependent RNA polymerase (RdRP) activity for amplification of small RNAs has been identified in insects [72,73]; however, it was proposed that reverse transcription of viral RNA by retrotransposons may result in viral cDNA elements serving as a template for the generation of new viRNAs [39]. In U4.4 cells it has been shown that siRNAs can spread through the culture if there is cell-to-cell contact, but cannot spread freely through the culture medium [6].…”