Is 3'UTR RNAi specific?


We’d like to silence the endogenous version of a gene while not silencing a transgenic C-term GFP fusion version of the gene. Does anyone know if this will work if we target the endogenous 3’UTR? Will the RNAi effect be specific?


RNAi in C. elegans can include a 3’ to 5’ RNA-dependent-RNA-polymerase (RDRP) activity, so targeting the 3’ UTR might cause the generation of siRNA from 5’ of that UTR, within the ORF. This would obviously be a problem for your application. I don’t know how frequently or strongly this occurs; why not give it a try, and see if it works?

You might also in theory be able to use a gfp fusion of a homologous gene from a closely related nematode (briggsae, say) that might be different enough at the nucleotide level to make cross-reacting RNAi less likely.

After I posted this question, I did find some papers reporting this transitive RNAi effect. It seems to be limited to 100-200 bp. Our 5’UTR is long, so this might work. Thanks,