(newbie) what makes siRNA and miRNA different - (Nov/09/2007 )
Hello,
there is some confusion in my head about why one group of short RNAs is called miRNA and another is called siRNA. I would be just as happy, if you could please point me to papers I should read before asking 
I read (in Zamore/Haley, 2005 Science) that "miRNAs and siRNAs are distinguished by their origins, not their functions".
So far, I thought that miRNAs come exclusively from miRNA genes (via pri-miRNA and pre-miRNA), but now I heard that they can come from introns, too (mirtrons, http://www.nature.com/nrg/journal/v8/n8/full/nrg2170.html ). So is it correct to say that miRNAs come from the DNA always and if something comes from the DNA, then it is a miRNA? Well, this is definitely not correct, I just don't know the right answer... I am simply trying to find some definition for miRNAs and siRNAs.
Btw, where do siRNAs come from? Other regions of the host organism's DNA (not coding miRNA genes or introns/exons)?
How did it happen that people started to use a new name (siRNA) instead of just using miRNA? If I understand correctly, Ambros & colleagues called lin-4 in 1993 a miRNA. "Later, the dsRNA was found to be converted into siRNAs -- fragments of the original dsRNA, 21 to 25 nt in length, that guide protein complexes to complementary mRNA targets, whose expression is then silenced (12-14)." (cite from Zamore/Haley 2005). Why did Refs.12-14 use the new name siRNA? What was the biological reason for them not to use the previously already used name miRNA?
Thanks for your time and answers in advance,
Illes
The term miRNA was not coined until after siRNA, even though you are quite correct in pointing out that lin-4 was discovered as a non-coding RNA before siRNA. But Ambros and Ruvkun groups didn't use the term miRNA. So that is why they didn't use miRNA. And I don't think it would be correct for them to use the term miRNA anyway, given that as you say, they are distinguished by their origins.
You are also quite right about all miRNAs coming from DNA, via pri-miRNA or mirtron processing. However, I believe that some siRNAs also are transcribed from DNA, although I think this is not the case in mammals, only plants ( - not so sure about this - hopefully others here can elaborate and/or correct me). In this case, I'm not sure how you would distinguish between miRNA and endogenous siRNA. Maybe evolutionary conservation of miRNA versus not for siRNA?
Hope this is of some help, hopefully others can also give some opinions.
http://www.protocol-online.org/biology-for...posts/5151.html
see these posts.