Intracellular localization and routing of miRNA and RNAi pathway components

Several different pathways, generally termed RNA silencing pathways, utilize small RNA molecules guiding sequence-specific silencing effects of ribonucleoprotein effector complexes, traditionally termed RNA-induced silencing complex (RISC). Three RNA silencing pathways were recognized in mammalian cells: RNA interference (RNAi), where short RNAs produced from long double-stranded RNA guide cleavage of cognate mRNAs, microRNA (miRNA) pathway, where endogenously-encoded miRNAs typically induce translational repression, and piRNA pathway, where piRNAs (PIWI-associated RNAs) guide repression of repetitive sequences in the germline. Originally, RNAi and miRNA pathways were thought to act in the cytoplasm, however, there is a growing body of evidence that these pathways also have a nuclear component. This text reviews the current evidence concerning nuclear localization and function of miRNA and RNAi pathway components. We provide evidence that TRBP, Dicer and AGO2, proteins found in the RISC-loading complex (RLC) and RISC itself, are present in the nucleus. Nonetheless, fully functional RLC is not found in the nuclear compartment which is consistent with the recent findings obtained by Fluorescence Cross-Correlation Spectroscopy experiments illustrating that RISC is specifically loaded within the cytoplasm and shuttles subsequently between the nuclear and cytoplasmic compartment, thereby allowing small RNA gene regulation in both compartments. The function of nuclear TRBP and Dicer proteins remains elusive. We also discuss the consequences of nucleotide analogs introduced into siRNAs which can severely interfere with the natural cytoplasmic localization mediated by Exportin-5 which is required for efficient RISC loading in the cytoplasm.