Plant Physiology Preview
Published on August 18, 2006; 10.1104/pp.106.083295
OPEN ACCESS ARTICLE
Received May 8, 2006
Accepted August 7, 2006
Computational estimation and experimental verification of off-target silencing during post-transcriptional gene silencing in plants
Ping Xu , Yuanji Zhang , Li Kang , Marilyn J. Roossinck , and Kirankumar S. Mysore *
Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401
* Corresponding author; email: ksmysore{at}noble.org.
Successful application of post-transcriptional gene silencing (PTGS) for gene function study in both plants and animals depends on high target specificity and silencing efficiency. By computational analysis with genome and/or transcriptome sequences of 25 plant species, we predicted that about 50-70% of gene transcripts in plants have potential off-targets when used for PTGS that could obscure experimental results. We have developed a publicly available web based computational tool called "siRNA Scan" to identify potential off-targets during PTGS. Some of the potential off-targets obtained from this tool were tested by measuring the amount of off-target transcripts using quantitative PCR. Up to 50% of the predicted off-target genes tested in plants was actually silenced when tested experimentally. Our results suggest that a high risk of off-target gene silencing exists during PTGS in plants. Our siRNA Scan tool is useful to design better constructs for PTGS by minimizing off-target gene silencing in both plants and animals.
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