newbie questions on RNAi / microRNAs - (Oct/11/2007 )
Dear Forum Members,
I am a postdoc in computational biology / statistical physics and I'm
trying to learn about microRNAs and the RNAi pathway. My apologies to
all of you for listing many questions below, I would be very grateful
for comments on even a few of them.
Thanks in advance for your time and comments,
Illes Farkas
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Illes Farkas
postdoctoral fellow
Eotvos University Email: fij@elte.hu
Dept. of Biological Physics Phone: +36-1-372-2768
Pazmany Peter setany 1A Fax: +36-1-372-2757
H1117 Budapest, Hungary Web: http://angel.elte.hu/fij
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1, Are multiple RISC complexes bound to a single mRNA molecule at the
same time?
2, The Pri-miRNA may contain more than one hairpin, and the Pre-miRNA
(after cleavage by Drosha) contains only one?
3, Is there a "rule of thumb" to decide which of the two strands in
the miRNA:miRNA* duplex is the miRNA strand and which is the miRNA*
strand?
4, Is there any physical difference between the two strands (miRNA and
miRNA*)?
5, After the miRNA is loaded into the RISC, the miRNA* strand is
discarded?
6, How long are mature plant miRNAs? Significantly longer than mature
animal miRNAs?
1. If there are multiple target sites in 1 3' UTR, then it is probable.
2. Hmm, if there are multiple miRNAs transcribed as 1 transcript from 1 cluster then yes. Otherwise, not sure.
3. The 1 with the highest stability at the 5' end is generally accepted to be the miRNA*
4. Not sure I understand...
5. Generally the miRNA* is degraded, although it has been cloned in a number of cases for different miRNAs, generally in large scale cloning efforts only.
6. I don't work with plant miRNAs, so I'm not sure.
Hope this helps
Dave
1, Are multiple RISC complexes bound to a single mRNA molecule at the
same time?
yes.
2, The Pri-miRNA may contain more than one hairpin, and the Pre-miRNA
(after cleavage by Drosha) contains only one?
Yes
3, Is there a "rule of thumb" to decide which of the two strands in
the miRNA:miRNA* duplex is the miRNA strand and which is the miRNA*
strand?
The strand with lower 5' stability is more likely the miRNA strand.
4, Is there any physical difference between the two strands (miRNA and
miRNA*)?
Apart from the thermodynamic property as stated in the answer to question 3, I don't know more.
5, After the miRNA is loaded into the RISC, the miRNA* strand is
discarded?
Agree with miRNA-man, but this question is not fully understood yet.
6, mature plant miRNAs are the same size of those of animals: most of them 21nt, some 20 or 22, a few 24. Pre-miRNAs can be much longer, ranging from 70nt to 500 or more.