Abstract
RNA interference (RNAi), mediated by short interfering RNAs (siRNAs), is one of the widely used functional genomics method for suppressing the gene expression in plants. Initially, gene silencing by RNAi mechanism was believed to be specific requiring sequence homology between siRNA and target mRNA. However, several recent reports have showed that non-specific effects often referred as off-target gene silencing can occur during RNAi. This unintended gene silencing can lead to false conclusions in RNAi experiments that are aimed to study the functional role of a particular target gene in plants. This especially is a major problem in large-scale RNAi-based screens aiming for gene discovery. Hence, understanding the off-target effects is crucial for minimizing such effects to better conclude gene function analyzed by RNAi. We discuss here potential problems of off-target gene silencing and focus on possibilities that favor this effect during post-transcriptional gene silencing. Suggestions to overcome the off-target effects during RNAi studies are also presented. We believe that information available in present-day plant science literature about specificity of siRNA actions is inadequate. In-depth systematic studies to understand their molecular basis are necessary to enable improved design of more specific RNAi vectors. In the meantime, gene function and phenotype results from present-day RNAi studies need to be interpreted with caution.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Waterhouse, P. M. and Helliwell, C. A. (2003) Exploring plant genomes by RNA-induced gene silencing. Nat. Rev. Genet. 4, 29–38.
Shuai, C., Daniel, H., Uwe, S., and Frederik, B. (2003) Temporal and spatial control of gene silencing in transgenic plants by inducible expression of double-stranded RNA. Plant J. 36, 731–740.
Auer, C. and Frederick, R. (2009) Crop improvement using small RNAs: applications and predictive ecological risk assessments. Trends Biotechnol. 27, 644–651.
Gordon, K. H. J. and Waterhouse, P. M. (2007) RNAi for insect-proof plants. Nat. Biotechnol. 25, 1231–1232.
Niu, Q.-W., Lin, S.-S., Reyes, J. L., Chen, K.-C., Wu, H.-W., Yeh, S.-D., and Chua, N.-H. (2006) Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat. Biotechnol. 24, 1420–1428.
Tang, G. and Galili, G. (2004) Using RNAi to improve plant nutritional value: From mechanism to application. Trends Biotechnol. 22, 463–469.
Jackson, A. L., Bartz, S. R., Schelter, J., Kobayashi, S. V., Burchard, J., Mao, M., Li, B., Cavet, G., and Linsley, P. S. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21, 635–637.
Xu, P., Zhang, Y., Kang, L., Roossinck, M. J., and Mysore, K. S. (2006) Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiol. 142, 429–440.
Jackson, A. L. and Linsley, P. S. (2004) Noise amidst the silence: off-target effects of siRNAs? Trends Genet. 20, 521–524.
Lin, X., Ruan, X., Anderson, M. G., McDowell, J. A., Kroeger, P. E., Fesik, S. W., and Shen, Y. (2005) siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucl. Acids Res. 33, 4527–4535.
Qiu, S., Adema, C. M., and Lane, T. (2005) A computational study of off-target effects of RNA interference. Nucl. Acids Res. 33, 1834–1847.
Saxena, S., Jónsson, Z., and Dutta, A. (2003) Small RNAs with imperfect match to endogenous mRNA repress translation. J. Biol. Chem. 278, 44312–44319.
Dunoyer, P., Himber, C., and Voinnet, O. (2005) DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat. Genet. 37, 1356–1360.
Agrawal, N., Dasaradhi, P. V. N., Mohmmed, A., Malhotra, P., Bhatnagar, R. K., and Mukherjee, S. K. (2003) RNA interference: biology, mechanism, and applications. Microbiol. Mol. Biol. Rev. 67, 657–685.
Meister, G. and Tuschl, T. (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343–349.
Bhaskar, P. B., Venkateshwaran, M., Wu, L., Ane, J.-M., and Jiang, J. (2009) Agrobacterium-mediated transient gene expression and silencing: a rapid tool for functional gene assay in potato. PLoS ONE 4, e5812.
Higuchi, M., Yoshizumi, T., Kuriyama, T., Hara, H., Akagi, C., Shimada, H., and Matsui, M. (2009) Simple construction of plant RNAi vectors using long oligonucleotides. J. Plant Res. 122, 477–482.
Senthil-Kumar, M., Hema, R., Suryachandra, T. R., Ramegowda, H. V., Gopalakrishna, R., Rama, N., Udayakumar, M., and Mysore, K. S. (2010) Functional characterization of three water deficit stress-induced genes in tobacco and Arabidopsis: an approach based on gene down regulation. Plant Physiol. Biochem. 48, 35–44.
Tang, W., Weidner, D. A., Hu, B. Y., Newton, R. J., and Hu, X.-H. (2006) Efficient delivery of small interfering RNA to plant cells by a nanosecond pulsed laser-induced stress wave for posttranscriptional gene silencing. Plant Sci. 171, 375–381.
Warthmann, N., Chen, H., Ossowski, S., Weigel, D., and Herve, P. (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS ONE 3, e1829.
Gheysen, G. and Vanholme, B. (2007) RNAi from plants to nematodes. Trends Biotechnol. 25, 89–92.
Wesley, S. V., Christopher, A. H., Neil, A. S., MingBo, W., Dean, T. R., Qing, L., Paul, S. G., Surinder, P. S., David, A., Peter, A. S., Simon, P. R., Andrew, P. G., Allan, G. G., and Peter, M. W. (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27, 581–590.
Filichkin, S. A., DiFazio, S. P., Brunner, A. M., Davis, J. M., Yang, Z. K., Kalluri, U. C., Arias, R. S., Etherington, E., Tuskan, G. A., and Strauss, S. H. (2007) Efficiency of gene silencing in Arabidopsis: direct inverted repeats vs. transitive RNAi vectors. Plant Biotechnol. J. 5, 615–626.
Stephan, O., Rebecca, S., and Detlef, W. (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 53, 674–690.
Carole, L. T., Louise, J., David, C. B., and Andrew, J. M. (2001) Size constraints for targeting post-transcriptional gene silencing and for RNA-directed methylation in Nicotiana benthamiana using a potato virus X vector. Plant J. 25, 417–425.
Bleys, A., Vermeersch, L., Van Houdt, H., and Depicker, A. (2006) The frequency and efficiency of endogene suppression by transitive silencing signals is influenced by the length of sequence homology. Plant Physiol. 142, 788–796.
Sijen, T., Fleenor, J., Simmer, F., Thijssen, K. L., Parrish, S., Timmons, L., Plasterk, R. H. A., and Fire, A. (2001) On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107, 465–476.
Kerschen, A., Napoli, C. A., Jorgensen, R. A., and Müller, A. E. (2004) Effectiveness of RNA interference in transgenic plants. FEBS Lett. 566, 223–228.
Kohli, A., Twyman, R. M., Abranches, R., Wegel, E., Stoger, E., and Christou, P. (2003) Transgene integration, organization and interaction in plants. Plant Mol. Biol. 52, 247–258.
Small, I. (2007) RNAi for revealing and engineering plant gene functions. Curr. Opin. Biotechnol. 18, 148–153.
Senthil-Kumar, M., Hema, R., Ajith, A., Li, K., Udayakumar, M., and Kirankumar, S. M. (2007) A systematic study to determine the extent of gene silencing in Nicotiana benthamiana and other Solanaceae species when heterologous gene sequences are used for virus-induced gene silencing. New Phytol. 176, 782–791.
Jackson, A. L., Burchard, J., Leake, D., Reynolds, A., Schelter, J., Guo, J., Johnson, J. M., Lim, L., Karpilow, J., Nichols, K., Marshall, W., Khvorova, A., and Linsley, P. S. (2006) Position-specific chemical modification of siRNAs reduces “off-target” transcript silencing. RNA 12, 1197–1205.
Van Houdt, H., Bleys, A., and Depicker, A. (2003) RNA target sequences promote spreading of RNA silencing. Plant Physiol. 131, 245–253.
Dimitri Semizarov, L. F., Aparna, S., Paul, K., Halbert, D. N., and Fesik, S. W. (2003) Specificity of short interfering RNA determined through gene expression signatures. Proc. Natl. Acad. Sci. USA 100, 6347–6352.
Khvorova, A., Reynolds, A., and Jayasena, S. D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216.
Muckstein, U., Tafer, H., Hackermuller, J., Bernhart, S. H., Stadler, P. F., and Hofacker, I. L. (2006) Thermodynamics of RNA–RNA binding. Bioinformatics 22, 1177–1182.
Birmingham, A., Anderson, E. M., Reynolds, A., Ilsley-Tyree, D., Leake, D., Fedorov, Y., Baskerville, S., Maksimova, E., Robinson, K., Karpilow, J., Marshall, W. S., and Khvorova, A. (2006) 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods 3, 199–204.
Dhirendra, K., Claes, G., and Daniel, F. K. (2006) Validation of RNAi silencing specificity using synthetic genes: salicylic acid-binding protein 2 is required for innate immunity in plants. Plant J. 45, 863–868.
Grimm, D., Streetz, K. L., Jopling, C. L., Storm, T. A., Pandey, K., Davis, C. R., Marion, P., Salazar, F., and Kay, M. A. (2006) Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 441, 537–541.
Acknowledgments
RNAi- and VIGS-related projects in KSM laboratory are supported by the Samuel Roberts Noble Foundation, National Science Foundation (grant no. 0445799), Oklahoma Center for the Advancement of Science and Technology (grant no. PSB09-020), and the US–Israel Binational Agricultural Research Development Fund (BARD grant no. IS-3922-06).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Senthil-Kumar, M., Mysore, K.S. (2011). Caveat of RNAi in Plants: The Off-Target Effect. In: Kodama, H., Komamine, A. (eds) RNAi and Plant Gene Function Analysis. Methods in Molecular Biology, vol 744. Humana Press. https://doi.org/10.1007/978-1-61779-123-9_2
Download citation
DOI: https://doi.org/10.1007/978-1-61779-123-9_2
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-122-2
Online ISBN: 978-1-61779-123-9
eBook Packages: Springer Protocols