Figure 1.
Core components of the Caenorhabditis elegans RNA interference (RNAi) pathway.
(1) Exogenously applied double-stranded RNA (dsRNA) and small interfering RNA (exo-siRNA) are thought to enter cells via SID (Systemic RNA Interference Defective) proteins SID-1/RSD-8 and SID-2. (2) Endogenous RNAi-based pathways begin in the nucleus; micro-interfering RNA (miRNA) synthesis begins with transcription of hairpin-looped primary miRNA (pri-miRNA) transcripts from intergenic, intronic or antisense regions. pri-miRNAs are processed by the DRSH-1/PASH-1 complex to pre-miRNA, which are exported from the nucleus by exportin proteins XPO-1, -2 and -3. Endogenous siRNAs (endo-siRNAs) are also produced from genomic regions, and exported by XPO-1, 2, and -3. (3) Both pre-miRNAs and exogenously applied dsRNA molecules are bound and cleaved by the dicer complex, which consists of the RNAse III-like nuclease DCR-1, the dsRNA-binding proteins RDE-1 and -4, the helicases DRH-1 and DRH-3/EKL-3, the RNA-dependent RNA-polymerase (RdRP) RRF-1, and the uncharacterized protein, AIN-1. Dicer cleaves dsRNA to produce siRNA molecules, and pre-miRNA to mature miRNA, both of which are substrates for the RNA-induced silencing complex (RISC). (4) Both siRNAs and miRNAs are the focus of a battery of inhibitors, which allow down-regulation of the RNAi response. (5) The RISC complex incorporates a single strand of miRNA or siRNA (termed the guide strand), and binds a complementary mRNA strand, eliciting gene silencing by either mRNA destruction or translational repression (6). The central catalytic component of RISC is an argonaute (AGO) protein, allied with the nuclease TSN-1, the RNA-binding protein VIG-1, and AIN-1. (7) The RNAi response may be amplified by the action of the RdRPs RRF-1 and -2, SMG-5, RDE-2/MUT-8 and MUT-7, which produce a population of single-stranded RNAs bearing N-terminal tri-phosphates from a target mRNA template. (8) These secondary siRNAs interact with Secondary-siRNA-specific AGOs (SAGO-1 and -2), terminating in down-regulation of target transcript. Secondary siRNAs can also spread between cells through RSD-2, -3 and -6, resulting in intercellular spread of the RNAi effect (9), and can be imported into the nucleus by NRDE-3, which elicits transcriptional silencing of nascent RNA transcripts as part of nuclear RISC (nucRISC) (10). siRNAs may also control aspects of nuclear RNAi, including histone methylation, chromatin formation and chromosome segregation (11). Dashed lines indicate miRNA-based pathways, solid lines indicate siRNA-based pathways.
Table 1.
Small RNA biosynthetic proteins.
Table 2.
dsRNA uptake and spreading, and siRNA amplification effectors.
Table 3.
Argonautes (AGOs) and RNA-induced Silencing Complex (RISC) components.
Table 4.
RNAi inhibitors.
Table 5.
Nuclear RNAi effectors.
Table 6.
Nematode RNAi effector protein complements.