RNAi of non-coding RNAs....? - (Oct/22/2008 )
Hi all!
I'm essentially new to the RNAi field, and would really appreciate any feedback/comments on a practical approach that would be really useful for a part of my project:
Is it at all possible to knock-down transcripts/transcription of a specific non-coding RNA? Or putting it in a different way: is there any way to introduce a siRNA or shRNA based on the sequence of a non-coding transcript to abrogate its endogenous role?
I would assume the introduction of an si/shRNA towards a transcript that is itself endogenously converted into an RNAi product would rather enhance the sequence-specific RNAi effect instead of abrogating it...? So is there maybe an alternative, sequence-specific approach to address this?
Hope that brabbling above makes any sense, if so, it would be great to read your thoughts/comments on it!
Thank you,
Jan
hi
i believe that you can use si/shRNA to knockdown noncoding rna because i know that in miRNA research field, people will use a tech called "AMO--anti-miRNA oligonucleotide" to target miRNA precusor or mature miRNA. I am not sure the chemical essence of AMO is DNA or RNA. You have to look it up yourself. But i am sure it is feasible to abrogate endogenous non-coding transcripts.
Guorong
I'm essentially new to the RNAi field, and would really appreciate any feedback/comments on a practical approach that would be really useful for a part of my project:
Is it at all possible to knock-down transcripts/transcription of a specific non-coding RNA? Or putting it in a different way: is there any way to introduce a siRNA or shRNA based on the sequence of a non-coding transcript to abrogate its endogenous role?
I would assume the introduction of an si/shRNA towards a transcript that is itself endogenously converted into an RNAi product would rather enhance the sequence-specific RNAi effect instead of abrogating it...? So is there maybe an alternative, sequence-specific approach to address this?
Hope that brabbling above makes any sense, if so, it would be great to read your thoughts/comments on it!
Thank you,
Jan
Excellent, thank you very much for the info! Found a few articles searching for AMO, and that seems to be a promising tool.
I think that one group made si/shRNAs directed against the hairpin part of the precursor miRNA to knock it down. I don't have the references to hand but I think it was a Nuc. Acids Res. or RNA paper, 2005 or 2006.
another technique call miRNA mimicry or sponge might also useful
http://www.nature.com/ng/journal/v39/n8/abs/ng2079.html
http://www.nature.com/nmeth/journal/v4/n9/.../nmeth1079.html
Yet another option is to bind a steric-blocking oligo to the pri-miRNA or pre-miRNA to inhibit processing by Dicer or Drosha.
Kloosterman WP, Lagendijk AK, Ketting RF, Moulton JD, Plasterk RH. Targeted Inhibition of miRNA Maturation with Morpholinos Reveals a Role for miR-375 in Pancreatic Islet Development. PLoS Biol. 2007 Jul 24;5(8):e203 [Epub ahead of print]
http://www.gene-tools.com/files/Kloosterman2007miRNA.pdf
Or to use a steric-blocking oligo to protect the miRNA targets on mRNA:
Choi WY, Giraldez AJ, Schier AF. Target Protectors Reveal Dampening and Balancing of Nodal Agonist and Antagonist by miR-430. Science. 2007 Oct 12;318(5848):271-4. Epub 2007 Aug 30.
http://www.ncbi.nlm.nih.gov/pubmed/17761850
Scroll down on this page for abstract-linked citations to papers using steric blocking oligos to block miRNA maturation and activity:
http://www.gene-tools.com/node/31
Willingham et al. (2005) made a large shRNA library against several ncRNAs:
http://www.scienceonline.org/cgi/content/full/309/5740/1570