what is the difference between miRNA and siRNA?

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MBer
MBer's picture
what is the difference between miRNA and siRNA?

It seems to me that those two are very similar. What is the difference? People seem to talk about those together.

jonmoulton
jonmoulton's picture
Hi MBer,

Hi MBer,

I heard this description at a developmental bio meeting and it seems to fit common usage.

siRNA is a synthetic molecule, consisting of double-stranded RNA with short single-stranded ends, which is transfected into cells and binds to RISC. siRNA is perfectly complementary to a particular target mRNA and cleaves that target. siRNA also suppresses translation of many off-target mRNAs that have partial sequence complementarity. The siRNA molecules may be indistinguishable from the double-stranded RNA molecules that are produced by the RNAi pathway, where Dicer cuts small (~21 base) chunks of dsRNA from a long piece of double-stranded RNA.

miRNA is a natural molecule, also consisting of double-stranded RNA with short single-stranded ends. Primary miRNA is transcribed from DNA and folds into a hairpin. The Drosha enzyme cuts the hairpin from the rest of the transcript, forming pre-miRNA. The Dicer enzyme cuts away the loop, forming the mature double-stranded miRNA. The double strand loads onto a complex which includes the Argonaute protein and Argonaute cleaves one strand of the dsRNA, incorporating the uncleaved single strand into the mature complex. This complex inhibits translation of partially-complementary mRNA.

The behavior of the two classes, siRNA and miRNA, is the same. Each can cleave perfectly complementary mRNA targets and decrease the expression of partially complementary targets. However, their origin is different, with siRNA an endogenous synthetic molecule and miRNA an endogenous genome-encoded molecule.

I hope more folks follow up on this, proposing alternative definitions; I am very interested in how these definitions are developing over time and I would be disappointed to have the last word here.

Regards,

- Jon

kumar
kumar's picture
I agree with Jon for the

I agree with Jon for the common usage of terms siRNA for exogenous synthetic and miRNA for endogenous genome-encoded silencing small RNAs. But after cursory literaure search it is clear that the usage of siRNA is not restricted to "synthetic" small RNAs:
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Nat Rev Mol Cell Biol. 2007 Jan;8(1):23-36.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17183358&query_hl=12&itool=pubmed_DocSum
"In addition to endogenous microRNAs (miRNAs) and exogenous small interfering (si)RNAs, which are discussed in the main text, endogenous siRNAs have been discovered in various organisms and fall into at least four classes: trans-acting siRNAs (tasiRNAs), repeat-associated siRNAs (rasiRNAs), small-scan (scn)RNAs and Piwi-interacting (pi)RNAs."

Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):18002-7
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17071740&query_hl=5&itool=pubmed_docsum
"Endogenous small interfering RNAs (siRNAs) and microRNAs (miRNAs) have emerged as important regulators of eukaryotic gene expression by guiding mRNA cleavage, translational inhibition, or chromatin modification (1, 2). In Arabidopsis, >100 miRNAs have been reported .. In contrast to the relatively limited number of miRNAs, thousands of endogenous siRNAs have been sequenced (6, 911). However, their biological roles are largely unknown except for the functions of transacting siRNAs (ta-siRNA) in plant development and hormone signaling (4) and the roles of some chromatin-associated siRNAs in DNA methylation and transcriptional gene silencing (4)."

Cell. 2006 Dec 15;127(6):1193-207
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17174894&query_hl=26&itool=pubmed_docsum
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.
"We sequenced approximately 400,000 small RNAs from Caenorhabditis elegans. Another 18 microRNA (miRNA) genes were identified, thereby extending to 112 our tally of confidently identified miRNA genes in C. elegans. Also observed were thousands of endogenous siRNAs generated by RNA-directed RNA polymerases acting preferentially on transcripts associated with spermatogenesis and transposons."
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The term miRNA was NEVER used for synthetic/exogenous silencing ( and the classification of topic miRNA under molecular biology, with siRNA, may be one reason for confusion!).

The major difference between endogenous siRNA and miRNA seems to be that the precursor of endogenous siRNA is a long dsRNA while the precursor of a miRNA is hairpin-shaped:

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Genes Dev. 2006 Jul 1;20(13):1709-14
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=16766680
"Small RNAs constitute a large family of regulatory molecules with diverse functions in eukaryotes. Hallmarks of small RNAs are their dependence on double-stranded RNAs (dsRNA)-specific RNase III-type enzymes for biogenesis and their association with Argonaute family proteins for the silencing process. At least two classes of small RNAs have previously been described: microRNAs (miRNAs) derived from hairpin-shaped precursors and small interfering RNAs (siRNAs) generated from long dsRNAs. Recent articles reported a novel class of small RNAs that are expressed specifically and abundantly in the spermatogenic cells of mice. These RNAs are bigger (26-31 nucleotides [nt]) than most previously described small RNAs (21-23 nt) and are associated with Piwi-subclade members of the Argonaute protein family. Although the biogenesis and function of these RNAs are yet to be determined, these findings may add new dimensions in small RNA biology and germline cell biology."
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To sum up:

Synthetic/exogenous small RNA molecule mediating gene silencing is termed siRNA.

Endogenous silencing small RNAs are termed: miRNAs when they are genetically encoded and have the potential to arise from foldback structures characteristic of miRNA precursor hairpins. siRNAs are similar small RNAs that do not appear to correspond to protein-coding regions and do not have the potential to arise from hairpins characteristic of miRNA precursors and yet are expressed at sufficiently high endogenous levels to be detected on RNA blots with the idea that they might be processed from long double-stranded RNA.

One important difference between siRNAs and miRNAs is a Nobel prize: Andy Fire and Craig Mello's discovery of RNAi is among the most important discoveries in molecular biology in the past few decades and was awarded the Nobel prize in Physiology/medicine for 2006. The discovery of miRNAs, originally made by Victor Ambros is equally important and deserving of recognition by the Nobel committee.

jonmoulton
jonmoulton's picture
Very nice, Kumar!

Very nice, Kumar!

The use of the term siRNA for both exogenous (from synthetic sources) and endogenous (from long dsRNA) short dsRNA is somewhat confusing, but I think that it is so thoroughly established that it is unlikely a clearer nomenclature will quickly supplant the current usage. Another confusing aspect of this nomenclature is the experimental use of short hairpin RNA, which can be transfected as an oligo or expressed in the target cell from a plasmid. Is this a subset of miRNA, of siRNA or it be classed separately as shRNA?

Thinking is easier when the nomenclature settles down.

- Jon

ryan_m
ryan_m's picture
jonmoulton wrote:Very nice,

jonmoulton wrote:

Very nice, Kumar!

The use of the term siRNA for both exogenous (from synthetic sources) and endogenous (from long dsRNA) short dsRNA is somewhat confusing, but I think that it is so thoroughly established that it is unlikely a clearer nomenclature will quickly supplant the current usage. Another confusing aspect of this nomenclature is the experimental use of short hairpin RNA, which can be transfected as an oligo or expressed in the target cell from a plasmid. Is this a subset of miRNA, of siRNA or it be classed separately as shRNA?

Thinking is easier when the nomenclature settles down.

- Jon

To confuse the matter, there is a large variety of classes of endogenous siRNAs (at least in plants). Trans-acting siRNAs target genes other than the one they derive from. Repeat-associated siRNAs (rasiRNAs) in animals and heterochromatin siRNAs (in plants) target chromatin modification in regions such as the centromeres where genomic repeats are concentrated. In this way, they can reduce expression of genes within a large chromosomal region rather than directing degradation of a single transcript. The endogenous siRNAs more commonly envisioned are the ones that derive from natural antisense transcripts (NAT's). These siRNAs basically knock down the gene from which one of the two strands of the double-stranded DCL/dicer target derive. There are both siRNA and microRNA vectors these days. It depends on what you want to do. Do you want to mimic the action of a microRNA by producing (you hope) only the ~22nt product in the cell? You would use a microRNA vector. Do you want to just knock down your gene of interest? Choose the good-old siRNA style and you should produce a plethora of siRNAs from one construct that 'hopefully' don't have off-target effects.

jonmoulton
jonmoulton's picture
ryan_m wrote: Do you want to

ryan_m wrote:

Do you want to just knock down your gene of interest? Choose the good-old siRNA style and you should produce a plethora of siRNAs from one construct that 'hopefully' don't have off-target effects.

An siRNA knockdown without off-target effects would be an unlikely outcome.

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.

Khatri
Khatri's picture
Hi,

Hi,
I would be very happy if any one explain the working mechanism of miRNA  other than RNAi pathway ?
 
Thanks
KC

jonmoulton
jonmoulton's picture
Here's a nice starting point,

Here's a nice starting point, from the latest Nature Reviews Genetics:
http://www.nature.com/nrg/posters/regulation/index.html

khola
khola's picture
 kindly help

 kindly help

vissu
vissu's picture
what are the possible

what are the possible problems for failure of shRNA to knockdown? Please kindly help me.

jyotiV
jyotiV's picture
 in lewin 10  si RNA and mi

 in lewin 10  si RNA and mi -RNa both are naturally occuring with a difference that mi RNA are more common and si RNA are produce on viral infections P.No 870