SMILE

Stochastic Models for the Inference of Life Evolution

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

Rual, J., Klitgord, N., Achaz, G.

BMC genomics

2007

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.

Bibtex

@article{rual_novel_2007,
Author = {Rual, Jean-François and Klitgord, Niels and Achaz,
Guillaume},
Title = {Novel insights into {RNAi} off-target effects using
{C}. elegans paralogs},
Journal = {BMC genomics},
Volume = {8},
Pages = {106},
Keywords = {Animals, Base Pair Mismatch, Caenorhabditis elegans,
Caenorhabditis elegans Proteins, Computational Biology,
Genetic Techniques, Models, Chemical, Ribonuclease III,
RNA, Double-Stranded, RNA Interference, RNA, Small
Interfering, Sensitivity and Specificity},
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.},
doi = {10.1186/1471-2164-8-106},
issn = {1471-2164},
language = {eng},
pmcid = {PMC1868761},
pmid = {17445269},
year = 2007
}

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