i’m working witha gene that has many isoforms and would like to do isoform specific rnai by generating double t7 clones to the various unique regions of each isoform. do people do this? i can’t seem to find a paper where this has been done. any experiences or a reference would be great.
In the Sijen et al. 2001 paper, you will see that the “spreading” of RNAi effects to nearby regions is distance-dependent. The RDRP activity will extend the siRNA toward the 5’-end of your gene, but its processivity appears weak. If the exons you want to leave untouched are far enough away (i.e., there are one or more large intervening introns) , you may be able to get isoform-specific knockdown.
RNAi of an upstream gene in the operon can induce the loss of function of the downstream gene. Such as RNAi lin-15b can induce ~95% Muv of eri-1(-) animals, which indicates the loss of functions of both lin-15b/lin-15a genes.