microRNA - gene expression mechanism (Apr/21/2010 )
I am quite confused about the differences between the mechanisms by which (i) antisense oligonucleotides, (ii) long dsRNA, and (iii) short 21-23 dsRNA act on RNAs to affect gene expression in human cells. I know the long dsRNA cause a broad effect, whereas the short dsRNA cause specific mRNA degradation.
However, I have come across many papers where long piece of dsRNA (in both worms or plants) activate the RNAi pathway, in where the long dsRNA gets cleaved into siRNA (20-25nt) and ultimately cause SPECIFIC mRNA degradation via RISC. Does this mean the exogenous siRNA should be classified as a long dsRNA? But long dsRNA cause broad/global effect!! I am confused...
(In addition, both siRNA and miRNA are in definition a size of 19-25nt, where both have larger sized precursors. I do need clarification on these definitions. )
Lastly, isn't miRNA as a definition a endogenous single-stranded RNA?
"Does this mean the exogenous siRNA should be classified as a long dsRNA?"
No, by definition, siRNA is short (approx. 19 - 23 bp) double-stranded, interfering RNA. "Long dsRNA" is not a very well defined term, but it usually means dsRNA longer than siRNA and usually more than 30 bp.
In worm and plant cells, long dsRNA can silence gene expression via the RNA interference pathway. However, in mammalian cells, long dsRNA triggers an interferon response and can lead to apoptosis. To avoid this response, siRNA's are transfected into mammalian cells to induce gene silencing via the RNA interference pathway.
miRNAs are a class of endogenous, regulatory short RNAs that function mostly via the RNA interference pathway. Wikipedia has a pretty good article on miRNAs. See: http://en.wikipedia.org/wiki/MicroRNA
Antisense oligos are synthetic oligomers designed to silence gene expression presumably by binding to complementary target mRNA and interfering with translation. Antisense oligos were developed before RNA interference became a hot area, and were not known to function via the RNA interference pathway, but they may do so - at least to some extent.