siRNA vs. miRNA - (Jul/04/2008 )
Hi,
Thanks for any comments you might have:
If I understand the abstracts of Horwich et.al (2007) Curr. Biol. http://www.ncbi.nlm.nih.gov/pubmed/17604629 and Forstemann et.al (2007) Cell http://www.ncbi.nlm.nih.gov/pubmed/17662943 correctly, then the difference betwen siRNA and miRNA is that siRNA is loaded into Ago2 and miRNA is loaded into Ago1. Is this definition true only for Drosophila or C.Elegans and H.sapiens also?
From Tomari et.al. (2004) Science http://www.ncbi.nlm.nih.gov/pubmed/15550672 :
Thermodynamic differences in the base-pairing stabilities of the 5' ends of the two approximately 21-nucleotide siRNA strands determine which siRNA strand is assembled into the RISC.
I heard the same about the difference between miRNA and miRNA*. Does this mean that there is no difference between the mechanisms how siRNA and miRNA are loaded into the RISC complexes and how the discarded * strand is selected?
Is it true that most short RNAs that can be loaded into Ago1 or Ago2 are loaded mainly into one of them ? In this case it would make sense to talk about "miRNA molecules" and "siRNA molecules".
Again, if I'm not mistaken, in Drosophila there are short RNA molecules that can be loaded into both Ago1 and Ago2. So it seems to be meaningless to talk about "miRNA molecules" and "siRNA molecules", but one should only talk about two pathways: Ago1-mediated and Ago2-mediated.
One major difference between Ago1 and Ago2 is that Ago1 allows mismatches, while Ago2 allow only perfect short RNA - mRNA pairs. I read that in plants usually perfect matches are used, while in animals usually imperfect matches. So is it true that plants use mainly Ago2 and animals use mainly Ago1 ?
As I understood, Ago2-mediated silencing is called RNAi (pathway). Does Ago1-mediated silencing have a similar name? (e.g., miRNA pathway)
Thanks for any comments you might have:
If I understand the abstracts of Horwich et.al (2007) Curr. Biol. http://www.ncbi.nlm.nih.gov/pubmed/17604629 and Forstemann et.al (2007) Cell http://www.ncbi.nlm.nih.gov/pubmed/17662943 correctly, then the difference betwen siRNA and miRNA is that siRNA is loaded into Ago2 and miRNA is loaded into Ago1. Is this definition true only for Drosophila or C.Elegans and H.sapiens also?
From Tomari et.al. (2004) Science http://www.ncbi.nlm.nih.gov/pubmed/15550672 :
Thermodynamic differences in the base-pairing stabilities of the 5' ends of the two approximately 21-nucleotide siRNA strands determine which siRNA strand is assembled into the RISC.
I heard the same about the difference between miRNA and miRNA*. Does this mean that there is no difference between the mechanisms how siRNA and miRNA are loaded into the RISC complexes and how the discarded * strand is selected?
Is it true that most short RNAs that can be loaded into Ago1 or Ago2 are loaded mainly into one of them ? In this case it would make sense to talk about "miRNA molecules" and "siRNA molecules".
Again, if I'm not mistaken, in Drosophila there are short RNA molecules that can be loaded into both Ago1 and Ago2. So it seems to be meaningless to talk about "miRNA molecules" and "siRNA molecules", but one should only talk about two pathways: Ago1-mediated and Ago2-mediated.
One major difference between Ago1 and Ago2 is that Ago1 allows mismatches, while Ago2 allow only perfect short RNA - mRNA pairs. I read that in plants usually perfect matches are used, while in animals usually imperfect matches. So is it true that plants use mainly Ago2 and animals use mainly Ago1 ?
As I understood, Ago2-mediated silencing is called RNAi (pathway). Does Ago1-mediated silencing have a similar name? (e.g., miRNA pathway)
I have no idea, but perhaps one of these lectures have an answer for you? Check some other keywords too.
http://search.vadlo.com/b/q?sn=158621799&a...A+ago&rel=2
..
Thanks. I guess, this is the major difference between mi and siRNAs:
There are mismatched and perfectly matched duplexes. The short regulating RNAs produced from the first group are called miRNAs, have additional loops and are loaded into Ago1. Those from second group have no loops, they are called siRNAs and are loaded into Ago2.
Is this correct ?
Thanks for any comments you might have:
If I understand the abstracts of Horwich et.al (2007) Curr. Biol. http://www.ncbi.nlm.nih.gov/pubmed/17604629 and Forstemann et.al (2007) Cell http://www.ncbi.nlm.nih.gov/pubmed/17662943 correctly, then the difference betwen siRNA and miRNA is that siRNA is loaded into Ago2 and miRNA is loaded into Ago1. Is this definition true only for Drosophila or C.Elegans and H.sapiens also?
From Tomari et.al. (2004) Science http://www.ncbi.nlm.nih.gov/pubmed/15550672 :
Thermodynamic differences in the base-pairing stabilities of the 5' ends of the two approximately 21-nucleotide siRNA strands determine which siRNA strand is assembled into the RISC.
I heard the same about the difference between miRNA and miRNA*. Does this mean that there is no difference between the mechanisms how siRNA and miRNA are loaded into the RISC complexes and how the discarded * strand is selected?
Is it true that most short RNAs that can be loaded into Ago1 or Ago2 are loaded mainly into one of them ? In this case it would make sense to talk about "miRNA molecules" and "siRNA molecules".
Again, if I'm not mistaken, in Drosophila there are short RNA molecules that can be loaded into both Ago1 and Ago2. So it seems to be meaningless to talk about "miRNA molecules" and "siRNA molecules", but one should only talk about two pathways: Ago1-mediated and Ago2-mediated.
One major difference between Ago1 and Ago2 is that Ago1 allows mismatches, while Ago2 allow only perfect short RNA - mRNA pairs. I read that in plants usually perfect matches are used, while in animals usually imperfect matches. So is it true that plants use mainly Ago2 and animals use mainly Ago1 ?
As I understood, Ago2-mediated silencing is called RNAi (pathway). Does Ago1-mediated silencing have a similar name? (e.g., miRNA pathway)
That's a lot of tough questions! I think that most of the questions are unanswered at the moment. I think that the Ago1/2 loading is only for Drosophila (at the moment). About your plant question, there is a recent paper (in Science, I think) showing that miRNA-mediated repression is actually quite common in plants. With your other questions, I have no idea, but they're very good questions
. hi there
i am new in RNA silencing strategies.
currently, I am trying to separate Small RNA from N.bentamiana infected with ACM virus by using denaturing polyacrylmide gel /Urea but it does work really well. what is your suggestion?
Another point, in parallell , i am transcribing siRNA by usng the protocol of invitrotranscriptin but it also does not result in a good and enough amount and quality yeild .
If you have experinced such stuff , could you say what is th optimal conditions to get high quality yeild of small RNA via invitrotranscription?
all the best,
Atef
i am new in RNA silencing strategies.
currently, I am trying to separate Small RNA from N.bentamiana infected with ACM virus by using denaturing polyacrylmide gel /Urea but it does work really well. what is your suggestion?
Another point, in parallell , i am transcribing siRNA by usng the protocol of invitrotranscriptin but it also does not result in a good and enough amount and quality yeild .
If you have experinced such stuff , could you say what is th optimal conditions to get high quality yeild of small RNA via invitrotranscription?
all the best,
Atef