Hello all,
What is the likelihood that the phenotype for an RNAi knockdown is not due the gene that we think we are targeting but rather another gene that exists together in an operon? In other words, can a single RNAi clone be responsible for knocking down multiple targets of a polycistronic cluster?
Thanks for any inputs !
If the targeting piece is in the downstream gene of the operon, the upstream gene can be affected in a process known as transitive RNAi. Off the top of my head I can think of one example of an operon where targeting one part of the operon affects the other gene - the lir-1/lin-26 operon . I’m sure there are others.
Do a little sleuthing and I’m sure you can find out more info. Google knows all! 
Thanks very much Steve, for the insights. The sleuthing that I initially did wasn’t very effective but you have pointed me in the right direction now (and confirmed my suspicion). Thank you!