General List of Off Target Effects of siRNA - (Oct/15/2007 )
I am looking to build up a list of genes that are regulated by all siRNA's. I know that most off target effects are caused by the specific sequence of the siRNA, but does anybody know the exact gene names of general off target effects.
Some of these might be useful. I think by "general off target effects" you mean what I categorize as non-antisense effects, which is the section toward the bottom of this list of citations. These tend to be weighted toward older papers, I've not tried to keep the list very current.
Specificity-----------------------------
Comparison of siRNA-induced off-target RNA and protein effects. Aleman LM, Doench J, Sharp PA. RNA. 2007 Jan 19; [Epub ahead of print]
Retraction of synapses and dendritic spines induced by off-target effects of RNA interference. Alvarez VA, Ridenour DA, Sabatini BL. J Neurosci. 2006 Jul 26;26(30):7820-5.
3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS, Khvorova A. Nat Methods. 2006 Mar;3(3):199-204.
Nonspecific, concentration-dependant stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). Persengiev SP, Zhu X and Green M. RNA 2004; 10:12-18.
Transcriptional gene silencing by short interfering RNAs. Kawasaki H, Taira K. Curr Opin Molec Therap. 2005 7(2):125-31.
Small interfering RNA-induced transcriptional gene silencing in human cells. Morris KV, Chan SWL, Jacobson SE, Looney DJ. Science 305(5688):1289-92.
A rapid and sensitive assay for quantification of siRNA efficiency and specificity. Smart N, Scambler PJ, Riley PR. Biol Proced Online. 2005;7:1-7. Epub 2005 Jan 24.
Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. Scacheri PC, Rozenblatt-Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, Hughes CM, Shanmugam KS, Bhattacharjee A, Meyerson M, Collins FS. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1892-7. Epub 2004 Feb 09.
Noise amidst the silence: off-target effects of siRNAs? Jackson AL, Linsley PS. Trends Genet. 2004 20(11):521-4
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.
Non-antisense effects-----------------------------
Synthetic double-stranded RNA induces multiple genes related to inflammation through Toll-like receptor 3 depending on NF-kappaB and/or IRF-3 in airway epithelial cells. Matsukura S, Kokubu F, Kurokawa M, Kawaguchi M, Ieki K, Kuga H, Odaka M, Suzuki S, Watanabe S, Takeuchi H, Kasama T, Adachi M. Clin Exp Allergy. 2006 Aug;36(8):1049-62.
Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Judge AD, Sood V, Shaw JR, Fang D, McClintock K, MacLachlan I. Nat Biotechnol. 2005 April;23(4):457-62.
Antisense and siRNA as agonists of Toll-like receptors. Agrawal S, Kandimalla ER. Nat Biotechnol. 2004 Dec;22(12):1533-7.
Small interfering RNAs mediate sequence-independent gene suppression and induce immune activation by signaling through toll-like receptor 3. Kariko K, Bhuyan P, Capodici J, Weissman D. J Immunol. 2004 Jun 1;172(11):6545-9.
Activation of the interferon system by short-interfering RNAs. Sledz CA, Holko M, de Veer MJ, Silverman RH, Williams BR. Nat Cell Biol. 2003 Sep;5(9):834-839.
Recognition of double-stranded RNA and activation of NF-kappaB by Toll-like receptor 3. Alexopoulou L, Holt AC, Medzhitov R, Flavell RA. Nature. 2001 Oct 18;413(6857):732-8.