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Novel insights into RNAi off-target effects using C. elegans paralogs.

ABSTRACT:

Background

In the few years since its discovery, RNAi has turned into a very powerful tool for the study of gene function by allowing post-transcriptional gene silencing. The RNAi mechanism, which is based on the introduction of a double-stranded RNA (dsRNA) trigger whose sequence is similar to that of the targeted messenger RNA (mRNA), is subject to off-target cross-reaction.

Results

We use a novel strategy based on phenotypic analysis of paralogs and predict that, in Caenorhabditis elegans, off-target effects occur when an mRNA sequence shares more than 95% identity over 40 nucleotides with the dsRNA. Interestingly, our results suggest that the minimum length necessary of a high-similarity stretch between a dsRNA and its target in order to observe an efficient RNAi effect varies from 30 to 50 nucleotides rather than 22 nucleotides, which is the length of siRNAs in C. elegans.

Conclusion

Our predictive methods would improve the design of dsRNA and ultimately the use of RNAi as a therapeutic tool upon experimental verification.

SUBMITTER: Rual JF

PROVIDER: S-EPMC1868761 | biostudies-literature | 2007 Apr

REPOSITORIES: biostudies-literature

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Novel insights into RNAi off-target effects using C. elegans paralogs.

Rual Jean-François JF Klitgord Niels N Achaz Guillaume G

BMC genomics 20070419

<h4>Background</h4>In the few years since its discovery, RNAi has turned into a very powerful tool for the study of gene function by allowing post-transcriptional gene silencing. The RNAi mechanism, which is based on the introduction of a double-stranded RNA (dsRNA) trigger whose sequence is similar to that of the targeted messenger RNA (mRNA), is subject to off-target cross-reaction.<h4>Results</h4>We use a novel strategy based on phenotypic analysis of paralogs and predict that, in Caenorhabdi ...[more]

PMID: 17445269

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