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

Ping Xu, Yuanji Zhang, Li Kang, Marilyn J. Roossinck, Kirankumar S. Mysore

Research output: Contribution to journalArticle

142 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)429-440
Number of pages12
JournalPlant physiology
Volume142
Issue number2
DOIs
StatePublished - Oct 1 2006

Fingerprint

RNA Interference
RNA interference
Gene Silencing
gene silencing
small interfering RNA
Small Interfering RNA
Genes
genes
Transcriptome
transcriptome
Reverse Transcription
animals
reverse transcriptase polymerase chain reaction
Genome
Polymerase Chain Reaction
genome

All Science Journal Classification (ASJC) codes

  • Physiology
  • Genetics
  • Plant Science

Cite this

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Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. / Xu, Ping; Zhang, Yuanji; Kang, Li; Roossinck, Marilyn J.; Mysore, Kirankumar S.

In: Plant physiology, Vol. 142, No. 2, 01.10.2006, p. 429-440.

Research output: Contribution to journalArticle

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