Mobile RNA reveal differential requirements for gene silencing in C. elegans at single-cell resolution

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Delivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the worm C. elegans, such organism-wide silencing relies on the transport of dsRNA to most cells and requires amplification mechanisms for effective gene silencing. Amplification of silencing signals is accomplished by two tissue-specific RNA-dependent RNA polymerases - EGO-1 in the germline and RRF-1 in somatic cells. Here, we reveal instances of RRF-1-independent silencing in somatic cells, which are dictated by three variables. First, when the same intestinal target gene was silenced using ingested, intestinal, or neuronal dsRNA, only silencing by mobile RNAs derived from neuronal dsRNA was independent of RRF-1. Second, when the same source of mobile RNA was used to silence a target sequence in different genomic contexts, the requirement for RRF-1 could change. Third, measurement of silencing by mobile RNAs at single-cell resolution revealed cell-to-cell and animal-to-animal variation in the requirement for RRF-1. Therefore, the requirements for gene silencing can vary based on the source of dsRNA, the target context, and even the particular cell examined, suggesting that each C. elegans animal is a functional mosaic with respect to RNA interference