Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants

Xu, Ping, Zhang, Yuanji, Kang, Li, Roossinck, Marilyn J and Mysore, Kirankumar S (2006) Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiology, 142 (2). pp. 429-440. ISSN 0032-0889

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Abstract

Successful application of posttranscriptional 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% to 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 reverse transcription-PCR. Up to 50% of the predicted off-target genes tested in plants were 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.

Item Type: Article
Uncontrolled Keywords: agrobacterium tumefaciens,animals,arabidopsis,gene expression regulation, plant,oryza,plant proteins,genetically modified plants,rna interference,reproducibility of results,software,tobacco
Depositing User: Pure Connector
Date Deposited: 21 Feb 2017 02:23
Last Modified: 22 Apr 2020 02:48
URI: https://ueaeprints.uea.ac.uk/id/eprint/62658
DOI: 10.1104/pp.106.083295

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