Fwd: RE: [Arabidopsis] Questions on plant RNAi

Dr. James J. Campanella via arab-gen%40net.bio.net (by james.campanella from montclair.edu)
Thu Aug 30 06:50:10 EST 2007


>Date: Wed, 29 Aug 2007 22:07:46 -0500
>From: "Subramanian, Senthil" <SSubramanian from danforthcenter.org>
>Subject: RE: [Arabidopsis] Questions on plant RNAi
>To: "Dr. James J. Campanella" <campanellj from mail.montclair.edu>
>Thread-topic: [Arabidopsis] Questions on plant RNAi
>Thread-index: AcfqhPOA8DtDMMdNTXa7edotNo6iyQALJYuO
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>Original-recipient: rfc822;james.campanella from montclair.edu
>
>Dr Campanella:
>
>Artificial miRNAs are very useful for silencing specific members of 
>gene families (much better than large RNAi constructs). Please refer 
>to the following publication.
>
>Rebecca Schwab, Stephan Ossowski, Markus Riester, Norman Warthmann, 
>and Detlef Weigel
>   Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis
>   Plant Cell 18: 1121-1133; First published on March 10, 2006; 
> 10.1105/tpc.105.039834
>
>Re. your other question about designing RNAi constructs for gene 
>silencing in plants, I am not aware of any reviews on the 
>methodology, but one of the landmark papers that you can refer to is
>
>Chuang CF, Meyerowitz EM (2000) Specific and heritable genetic 
>interference by double-stranded RNA in Arabidopsis thaliana. Proc 
>Natl Acad Sci USA 97: 4985-4990
>Hope this helps,
>
>Sen Subramanian
>Donald Danforth Plant Science Center,
>St Louis, MO
>
><http://www.knowplants.org>www.knowplants.org
>
>
>----------
>From: arab-gen-bounces from oat.bio.indiana.edu on behalf of Dr. James J. 
>Campanella
>Sent: Wed 8/29/2007 8:55 AM
>To: arab-gen from magpie.bio.indiana.edu; 
>plantbio from magpie.bio.indiana.edu; methods from oat.bio.indiana.edu
>Subject: [Arabidopsis] Questions on plant RNAi
>
>Dear Colleagues,
>
>I have several questions about practical plant RNAi to which I have
>been unable to find the answers in the literature. I suspect that
>these questions are mostly naive, but I since none of my colleagues
>here on my own campus work with plant RNAi, I thought I may be able
>to find the answers out here.
>
>First, are there any good practical guides or reviews out there on
>plant RNAi? Most of the literature that I have been able to dig up is
>on animal RNAi which is quite different in terms of RNAi probe design
>and activity. So far, the most practical advice has come from the
>Methods in Enzymology volume on RNAi.
>
>Second, again, there is a great deal of literature on designing the
>short RNAi probes for animals. There are even computer programs to
>help design those short sequences. However, I have been unable to
>come across any advice on choosing the long (300-500 bp) sequences
>needed for plant RNAi.
>
>Third, I am working with a family of plant genes, and I want to be
>able to knock down specific members of that family. What is the
>breakpoint percentage of homology at which you need no longer worry
>about cross-over inhibition against homologues? If the probe is 50%
>homologous to another family member which is not the target, will you
>get knockdown of the homologue? 40%? 30%? Is this even common
>knowledge, or does it come down to finding out these answers by
>practical experiments with your own species and gene family?
>
>Thanks for the help,
>
>Jim Campanella
>
>
>James J. Campanella,
>Associate Professor,
>Department of Biology and Molecular Biology
>Montclair State University
>1 Normal Avenue
>Montclair, NJ 07043
>
>Alternate email address: jcamp from alumni.uchicago.edu
>
>Ph: 973-655-4097
>Fax: 973-655-7047
>
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James J. Campanella,
Associate Professor,
Department of Biology and Molecular Biology
Montclair State University
1 Normal Avenue
Montclair, NJ 07043

Alternate email address: jcamp from alumni.uchicago.edu

Ph: 973-655-4097
Fax: 973-655-7047 



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