shRNA designed for AB1 gene also knockdown AB2 - (Nov/08/2012 )

I recently encoutered a mystery that my shRNA containing lentivirus knocked-down AB1 gene (a pseudoname) but also knocked down another homologue, AB2. How could this happen? I thought shRNA (designed by TRC) is very specific.

Have you checked the shRNA sequence to see if it targets AB2? You said the two genes are homologue, it is more often than not they share some sequence homology. the shRNA could have an effect on genes with which there is only partial homology.

This sort of effect is well documented. If a non-native sequence loads onto RISC, you will get off-target gene modulation.

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Small interfering RNA-induced transcriptional gene silencing in human cells. Morris KV, Chan SWL, Jacobson SE, Looney DJ. Science 2004 Aug 27;305(5688):1289-92. Epub 2004 Aug 5.

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Expression profiling reveals off-target gene regulation by RNAi. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS. Nat Biotechnol. 2003 Jun;21(6):635-637.

Small RNAs with Imperfect Match to Endogenous mRNA Repress Translation: Implications for off-target activity of small inhibitory RNA in mammalian cells. Saxena S, Jonsson ZO, Dutta A. J Biol Chem. 2003 Nov 7;278(45):44312-44319.