we have been trying to determine the cleavage sites of our target mRNA by siRNA peoduced from our RNAi construct introduced into the transgenic plants. Using 5' RACE we detected several cleavage sites along our mRNA target sequence in our transgenic plants. As a control, we also examined the wild type mRNA of the same gene. We thought the wild type mRNA of the same gene should not be cleaved, but should go through RNA decade which is not detectable. However, we found several cleavage sites of the mRNA in wild type plant. Of these, one cleavage site is located at the precise location as the cleavage site by siRNA and remaining cleavage sites are located different from those sites by siRNA of transgenic plants.
How come did the wild type mRNA show also cleavage without transgenic expression of RNAi cassette generating siRNA? Did we do any thing wrong or such cleavage of the mRNA of the same gene in wild type plant is normal?
Will greatly appreciate any clue/suggestion.