RNA interference: a multifaceted innate antiviral defense

RNA interference (RNAi) is a highly conserved mechanism for gene silencing in higher eukaryotes [1]. RNAi-based gene silencing utilizes 21-nucleotide duplexes (short interfering RNA or siRNA) consisting of 19 base pairs with 2 nucleotides overhanging each 3' ends. These are derived from longer double-stranded RNA by sequential cleavage with the RNase III enzymes, Drosha and Dicer [2-5]. The microRNAs (miRNAs) are transcribed as mRNA-like primary miRNA (pri-miRNA) and then processed by the nuclear enzyme Drosha into shorter stem-loop structures (pre-miRNAs) that are exported from the nucleus to the cytoplasm, where they are cleaved by Dicer to yield ~21–23 nucleotide long miRNAs containing 5'-phosphate and 3'-hydroxyl termini [2]. Although the two small RNAi effecter molecules have different origins (siRNA is derived from double-stranded RNA transcripts and miRNAs are derived from longer stem-loop structures), both are incorporated into the RNA-induced silencing complex (RISC) for mRNA targeting. In practice, synthetic siRNA duplexes are widely used for loss of function analysis, while endogenous RNAi utilizes miRNAs [6].Unlike the perfect base-complementarity of the siRNA 'guide' strand and its target mRNA, miRNAs bind their target mRNAs primarily through their 5' nucleotides 2–7, also known as the "seed" sequence. Base-pairing at the seed sequence is important for miRNA-mRNA interaction. However, perfect seed sequence pairing is not always essential for effective translational inhibition of the target mRNA by the miRNA. Thus, a single miRNA could regulate multiple mRNA targets during the stress response [7], and conversely, host miRNAs could target viral RNAs synthesized in mammalian cells in order to defend against infection [8,9].A number of recent studies using primary cells have shown that the innate RNAi response is an important component of the mammalian antiviral response. This conclusion was reached based on several findings. Firstly, depletion of RNAi func