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My textbook says that in RNAi, a complementary double stranded RNA sequence attaches to an mRNA and silences it using a protein machinery. I Googled and read about this so now I know what siRNA and RISC and microRNA are. But the next thing my book says is

the source of these complementary double stranded RNA sequence [obviously my textbook means siRNA] may be viruses and transposable elements.”

What does this mean? Do transposons make siRNA? I thought transposons were non-coding except when they travel via the retrotransposon mechanism.

Do viruses that infect eukaryotic cells donate their own RNA genetic material for the cell to use in RNAi? But I thought RNAi was a cellular defence against viruses, how can viruses help give the dsRNA that’s supposed to fight the viruses? A number of sites online simply state that siRNA is exogenous is origin; do they mean that it comes from viruses?

I would greatly appreciate it if someone could take the time to answer each of my questions one by one or even recommend a site that answers them all.

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  • $\begingroup$ Which textbooks do you use? For instance, Stryer/Berg, 6th ed. on "RNA intereference" does not even tell about the origin of dsRNS. In my answer to some biology.stackexchange.com/questions/95306/… I just added my "learning thesis" that incoming sRNA (in case of sRNS-viruses) might just be duplicated to dsRNA by some RNA dependent RNA polymerase (which does exist: "RNS polymerase II", by the way).Existence of physiological functions of RNAi should imply endogenous origin, though. Just the opposite to viral defence. $\endgroup$ – Peter Bernhard Jan 4 at 11:39
  • $\begingroup$ "thought transposons were non-coding except when they travel via the retrotransposon mechanism" - I am not, are you, sure about the terming "non coding": isn't that word restricted to coding of proteins in contrast to coding of mRNA. (This terminological problem might be separated from "sense/anti-sense" - template learning problem) . So in a wider sense the fact that transposons are called non coding does not hinder their coding for RNA that does not end up being translated to proteins. Then, "that is the question", yours, if transposons do code for dsRNS being used for RNAi. $\endgroup$ – Peter Bernhard Jan 4 at 11:44
  • $\begingroup$ "....how can viruses help give the dsRNA that’s supposed to fight the viruses?" Now, that is a very pacifist way to put it - hoping you letting me put that to you:-() $\endgroup$ – Peter Bernhard Jan 4 at 11:47
  • $\begingroup$ tHello, your textbook is "Karp, Cell biology"? $\endgroup$ – Peter Bernhard Jan 7 at 18:59
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Transposons and viruses don't "make siRNA". However, an endonuclease called Dicer can process dsRNA from these sources to produce siRNA which is then loaded to the RNA-induced silencing complex (RISC) to suppress propagation of viruses and transposons. The following papers provide a good overview:

Buchon N, Vaury C. 2006. RNAi: a defensive RNA-silencing against viruses and transposable elements. Heredity 96:195-202.

van Rij RP, Andino R. 2006. The silent treatment: RNAi as a defense against virus infection in mammals. Trends Biotechnol 24:186-193.

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  • $\begingroup$ Not sure how much of an explanation you are looking for since this is well covered on Wikipedia and in scientific literature. If you want me to elaborate on something, let me know. $\endgroup$ – canadianer Oct 6 '17 at 18:24
  • $\begingroup$ Thank you for the site-links, I read them and it’s safe to say, I have a fair idea now. $\endgroup$ – Inkjet Oct 8 '17 at 9:01
  • $\begingroup$ @Inkjet Refering to "A number of sites online simply state that siRNA is exogenous is origin; do they mean that it comes from viruses?" As a beginner I read about "injecting" dsRNA - anyway, you speak of "exogenous", I read in sources of "environmental dsRNA"? Can you now say what that is? To my beginner's mind there is a whole lot of necrosis and debris around...Thank you! (must read the sources given here, for hasty people answer might be helpful hint). $\endgroup$ – Peter Bernhard Dec 28 '20 at 14:54
  • $\begingroup$ In a very sensational mood I hereby thank you for apparently inspiring my thinking in biology.stackexchange.com/questions/95306/… by doing your good citation work. With first time reading and less knowledge one may easily ignore what's in that title "...against viruses and transposable elements." That means RNAi is some military police against messing up of transposons. Thus, transposons are some home virus - or, is it transposons fighting each other?! I will read your reference. $\endgroup$ – Peter Bernhard Jan 4 at 11:56
  • $\begingroup$ first link you gave "page not found" $\endgroup$ – Peter Bernhard Jan 4 at 11:57

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