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siRNA vs miRNA

siRNA vs miRNA - RNA Techniques Forum

siRNA vs miRNA - Post and discuss RNA methods and RNA science related topics. RNA extraction, cDNA synthesis, RNA EMSA, and other RNA protocols.


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  #1  
Old 05-18-2009, 04:04 PM
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Default siRNA vs miRNA



Hi friends,

Tell me whether siRNA based gene silencing is more effective or miRNA based.How miRNA gene silencing is activated and siRNA is? Thanks.
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Old 05-19-2009, 05:04 PM
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Default Re: siRNA vs miRNA

Quote:
Originally Posted by Barbienidoo View Post
Hi friends,

Tell me whether siRNA based gene silencing is more effective or miRNA based.How miRNA gene silencing is activated and siRNA is? Thanks.

Hi Barbienidoo,

OK, I'll undertake some careful definitions; assuming we agree on these, I'll try a few statements which might useful.

First we need to understand what you mean by siRNA and miRNA. As I understand it, when double stranded RNA is introduced into cells as oligos it is siRNA. When it is introduced as hairpins (shRNA) that is also a class of siRNA. I think hairpin RNA that forms though transcription from an exogenous plasmid and then is processed by Drosha and Dicer and loaded onto RISC is also considered a form of siRNA.

However, when a RNA is transcribed from a chromosome, forms a stem-loop and is processed by Drosha and Dicer and loaded onto RISC, this is called a miRNA.

The difference is in where the RNA comes from. Transcription from endogenous DNA can produce miRNA, transcription from exogenous DNA can form siRNA and introduction of hairpins or dsRNA oligos are also forms of siRNA.

Now, if that matches your definitions of siRNA and miRNA then we can say that either is as effective against their targets once they are loaded onto the RISC; after all, RNA is RNA. Efficacy of loading might differ between dsRNA oligos and shRNA, as cleavage by Dicer is thought to position the new dsRNA for efficient loading onto RISC. The degree of complementarity with MRE on mRNAs will affect efficacy of knockdown.

Both miRNA and siRNA will modulate expression of many genes; in the case of miRNA, this network of gene modulation is tuned by natural selection while in the case of siRNA, you may get unanticipated effects. The RNA is just RNA regardless of where it comes from, but the endogenous sequences have evolved relationships with the transcriptome while the exogenous sequences trigger surprises.

Here are some citations that address the off-target gene modulation encountered with siRNA and the networks of gene modulation controlled by miRNA. siRNA is an effective system for achieving about 80% knockdown of a target gene, but be careful with your controls!

Widespread changes in protein synthesis induced by microRNAs. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Nature. 2008 Jul 30. [Epub ahead of print]

Comparison of siRNA-induced off-target RNA and protein effects. Aleman LM, Doench J, Sharp PA. RNA. 2007 Jan 19; [Epub ahead of print]

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.

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.

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.
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Old 11-22-2011, 01:18 PM
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Default Re: siRNA vs miRNA

Hello, I read that antisense strand of sirna actually binds with mRNA, but please look at the following example from Tuschl lab page.

Human lamin B1
targeted region (cDNA): 5' AACGCGCTTGGTAGAGGTGGATT (1)
sense siRNA: 5' CGCGCUUGGUAGAGGUGGAdTdT (2)
antisense siRNA: 5' UCCACCUCUACCAAGCGCGdTdT (3)

here antisense siRNA is complimentary to the cDNA, so it could not bind to mRNA, in fact sense strand of the siRNA binds to mRNA??

Please correct me if I am wrong,
There are some more examples on Tuschl lab pagerockefeller.edu/labheads/tuschl/sirna.html).

Regards
Kumar
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Old 12-02-2011, 03:56 PM
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Default Re: siRNA vs miRNA

Hi Kumar,

I addressed your question here:
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