title: Dicer-2 processes diverse viral RNA species.
abstract: RNA silencing pathways play critical roles in gene regulation, virus infection, and transposon control. RNA interference (RNAi) is mediated by small interfering RNAs (siRNAs), which are liberated from double-stranded (ds)RNA precursors by Dicer and guide the RNA-induced silencing complex (RISC) to targets. Although principles governing small RNA sorting into RISC have been uncovered, the spectrum of RNA species that can be targeted by Dicer proteins, particularly the viral RNAs present during an infection, are poorly understood. Dicer-2 potently restricts viral infection in insects by generating virus-derived siRNAs from viral RNA. To better characterize the substrates of Dicer-2, we examined the virus-derived siRNAs produced during the Drosophila antiviral RNAi response to four different viruses using high-throughput sequencing. We found that each virus was uniquely targeted by the RNAi pathway; dicing substrates included dsRNA replication intermediates and intramolecular RNA stem loops. For instance, a putative intergenic RNA hairpin encoded by Rift Valley Fever virus generates abundant small RNAs in both Drosophila and mosquito cells, while repetitive sequences within the genomic termini of Vaccinia virus, which give rise to abundant small RNAs in Drosophila, were found to be transcribed in both insect and mammalian cells. Moreover, we provide evidence that the RNA species targeted by Dicer-2 can be modulated by the presence of a viral suppressor of RNAi. This study uncovered several novel, heavily targeted features within viral genomes, offering insight into viral replication, viral immune evasion strategies, and the mechanism of antiviral RNAi.
authors: Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors: Leah R
authors: LR
authors: Sabin
authors: Qi
authors: Q
authors: Zheng
authors: Pramod
authors: P
authors: Thekkat
authors: Jamie
authors: J
authors: Yang
authors: Gregory J
authors: GJ
authors: Hannon
authors: Brian D
authors: BD
authors: Gregory
authors: Matthew
authors: M
authors: Tudor
authors: Sara
authors: S
authors: Cherry
mesh_terms: D000818:Animals; D029721:Drosophila Proteins / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000201:enzymology / Q000821:virology; D016679:Genome, Viral / Q000235:genetics; D023281:Genomics; D055029:Inverted Repeat Sequences; D020365:RNA Helicases / Q000378:metabolism*; D034622:RNA Interference; D012323:RNA Processing, Post-Transcriptional; D012328:RNA Viruses / Q000235:genetics; D012330:RNA, Double-Stranded / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism*; D043244:Ribonuclease III / Q000378:metabolism*
chemical_list: D029721:Drosophila Proteins; D012330:RNA, Double-Stranded; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D012367:RNA, Viral; C478069:DCR-2 protein, Drosophila; D043244:Ribonuclease III; D020365:RNA Helicases