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Considering RNAi experimental design in parasitic helminths

Published online by Cambridge University Press:  05 January 2012

JOHNATHAN J. DALZELL ,
NEIL D. WARNOCK ,
PAUL MCVEIGH ,
NIKKI J. MARKS ,
ANGELA MOUSLEY ,
LOUISE ATKINSON  and
AARON G. MAULE
JOHNATHAN J. DALZELL
Affiliation:
Molecular Biosciences-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL
NEIL D. WARNOCK
Affiliation:
Molecular Biosciences-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL
PAUL MCVEIGH
Affiliation:
Molecular Biosciences-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL
NIKKI J. MARKS
Affiliation:
Molecular Biosciences-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL
ANGELA MOUSLEY
Affiliation:
Molecular Biosciences-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL
LOUISE ATKINSON
Affiliation:
Molecular Biosciences-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL
AARON G. MAULE*
Affiliation:
Molecular Biosciences-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL
*
*Corresponding author: School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK. Tel: +44 (0)28 9097 2059. Fax: +44 (0)28 9097 5877. E-mail: [email protected]
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Summary

Almost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.

Keywords

Gene silencingdouble stranded RNAshort interfering RNARNAi controlRNAi validation
Type
Research Article
Information
Parasitology , Volume 139 , Special Issue 5: Genetic manipulation of parasitic helminths to define gene function , April 2012 , pp. 589 - 604
Copyright
Copyright © Cambridge University Press 2012

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References

REFERENCES

Ahringer, J. (2006). Reverse genetics. In Wormbook (ed. the C. elegans research community), doi/10.1895/wormbook.1.47.1, http://www.wormbook.org.Google Scholar
Alder, M. N., Dames, S., Gaudet, J. and Mango, S. E. (2003). Gene silencing in Caenorhabditis elegans by transitive RNA interference. RNA 9, 25–32.CrossRefGoogle ScholarPubMed
Ambardekar, V. V., Han, H. Y., Varney, M. L., Vinogradov, S. V., Singh, R. K. and Vetro, J. A. (2011). The modification of siRNA with 3′ cholesterol to increase nuclease protection and suppression of native mRNA by select siRNA polyplexes. Biomaterials 32, 1404–1411.CrossRefGoogle ScholarPubMed
Aoki, K., Moriguchi, H., Yoshioka, T., Okawa, K. and Tabara, H. (2007). In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO Journal 26, 5007–5019.CrossRefGoogle ScholarPubMed
Arora, A., Guduric-Fuchs, J., Harwood, L., Dellett, M., Cogliati, T. and Simpson, D. A. (2010). Prediction of microRNAs affecting mRNA expression during retinal development. BMC Developmental Biology 10, 1.CrossRefGoogle ScholarPubMed
Atkinson, L. E., McVeigh, P., Kimber, M. J., Marks, N. J., Eipper, B. A., Mains, R. E., Day, T. A. and Maule, A. G. (2010). A PAL for Schistosoma mansoni PHM. Molecular and Biochemical Parasitology 173, 97–106.CrossRefGoogle ScholarPubMed
Bakhetia, M., Urwin, P. E. and Atkinson, H. J. (2008). Characterisation by RNAi of pioneer genes expressed in the dorsal pharyngeal gland cell of Heterodera glycines and the effects of combinatorial RNAi. International Journal for Parasitology 38, 1589–1597.CrossRefGoogle ScholarPubMed
Bartlett, D. W. and Davis, M. E. (2006). Insights into the kinetics of siRNA-mediated gene silencing from live-cell and live-animal bioluminescent imaging. Nucleic Acids Research 34, 322–333.CrossRefGoogle ScholarPubMed
Bramsen, J. B., Pakula, M. M., Hansen, T. B., Bus, C., Langkjaer, N., Odadzic, D., Smicius, R., Wengel, S. L., Chattopadhyaya, J., Engels, J. W., Herdewijn, P., Wengel, J. and Kjems, J. (2010). A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects. Nucleic Acids Research 38, 5761–5773.CrossRefGoogle ScholarPubMed
Bustin, S. A. (2000). Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Journal of Molecular Endocrinology 25, 169–193.CrossRefGoogle ScholarPubMed
Caffrey, C. R., Rohwer, A., Oellien, F., Marhofer, R. J., Braschi, S., Oliveira, G., McKerrow, J. H. and Selzer, P. M. (2009). A comparative chemogenomics strategy to predict potential drug targets in the metazoan pathogen, Schistosoma mansoni. PLoS One 4, e4413.CrossRefGoogle ScholarPubMed
Calixto, A., Chelur, D., Topalidou, I., Chen, X. and Chalfie, M. (2010). Enhanced neuronal RNAi in C. elegans using SID-1. Nature Methods 7, 554–559.CrossRefGoogle Scholar
Clark, S. J., Statham, A., Stirzaker, C., Molloy, P. L. and Frommer, M. (2006). DNA methylation: Bisulphite modification and analysis. Nature Protocols 1, 2353–2364.CrossRefGoogle ScholarPubMed
Dalzell, J. J., McMaster, S., Fleming, C. C. and Maule, A. G. (2010a). Short interfering RNA-mediated gene silencing in Globodera pallida and Meloidogyne incognita infective stage juveniles. International Journal for Parasitology 40, 91–100.CrossRefGoogle ScholarPubMed
Dalzell, J. J., McMaster, S., Johnston, M. J., Kerr, R., Fleming, C. C. and Maule, A. G. (2009). Non-nematode-derived double-stranded RNAs induce profound phenotypic changes in Meloidogyne incognita and Globodera pallida infective juveniles. International Journal for Parasitology 39, 1503–1516.CrossRefGoogle ScholarPubMed
Dalzell, J. J., McVeigh, P., Warnock, N. D., Mitreva, M., Bird, D. M., Abad, P., Fleming, C. C., Day, T. A., Mousley, A., Marks, N. J. and Maule, A. G. (2011). RNAi effector diversity in nematodes. PLoS Neglected Tropical Diseases 5, e1176.CrossRefGoogle ScholarPubMed
Dalzell, J. J., Warnock, N. D., Stevenson, M. A., Mousley, A., Fleming, C. C. and Maule, A. G. (2010b). Short interfering RNA-mediated knockdown of drosha and pasha in undifferentiated Meloidogyne incognita eggs leads to irregular growth and embryonic lethality. International Journal for Parasitology 40, 1303–1310.CrossRefGoogle ScholarPubMed
Douthart, R. J. and Burgett, S. G. (1978). Enzymatic degradation by the sera of various animal species of Penicillium chrysogenum mycophage double-stranded RNA. Biochemical and Biophysical Research Communications 84, 809–815.CrossRefGoogle ScholarPubMed
Dubreuil, G., Deleury, E., Magliano, M., Jaouannet, M., Abad, P. and Rosso, M. (2011). Peroxiredoxins from the plant parasitic root-knot nematode, Meloidogyne incognita, are required for successful development within the host. International Journal for Parasitology 41, 385–396.CrossRefGoogle ScholarPubMed
Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W. and Tuschl, T. (2001). Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO Journal 20, 6877–6888.CrossRefGoogle ScholarPubMed
Fanelli, E., DiVito, M., Jones, J. and DeGiorgi, C. (2005). Analysis of chitin synthase function in a plant parasitic nematode, Meloidogyne artiellia, using RNAi. Gene 349, 87–95.CrossRefGoogle Scholar
Fedorov, Y., Anderson, E. M., Birmingham, A., Reynolds, A., Karpilow, J., Robinson, K., Leake, D., Marshall, W. S. and Khvorova, A. (2006). Off-target effects by siRNA can induce toxic phenotype. RNA 12, 1188–1196.CrossRefGoogle ScholarPubMed
Feinberg, E. H. and Hunter, C. P. (2003). Transport of dsRNA into cells by the transmembrane protein SID-1. Science 301, 1545–1547.CrossRefGoogle ScholarPubMed
Geldhof, P., Murray, L., Couthier, A., Gilleard, J., McLauchlan, G., Knox, D. and Britton, C. (2006). Testing the efficacy of RNA interference in Haemonchus contortus. International Journal for Parasitology 36, 801–810.CrossRefGoogle ScholarPubMed
Geldhof, P., Visser, A., Clark, D., Saunders, G., Britton, C., Gilleard, J., Berriman, M. and Knox, D. (2007). RNA interference in parasitic helminths: Current situation, potential pitfalls and future prospects. Parasitology 134, 609–619.CrossRefGoogle ScholarPubMed
Gent, J. I., Lamm, A. T., Pavelec, D. M., Maniar, J. M., Parameswaran, P., Tao, L., Kennedy, S. and Fire, A. Z. (2010). Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. Molecular Cell 37, 679–689.CrossRefGoogle Scholar
Geyer, K. K., Rodriguez, C. M., Chalmers, I. W., Munshi, S. E., Truscott, M., Heald, J., Wilkinson, M. J. and Hoffman, K. F. (2011). Cytosine methylation regulates oviposition in the pathogenic blood fluke Schistosoma mansoni. Nature Communications 2, 424.CrossRefGoogle ScholarPubMed
Ghildiyal, M., Xu, J., Seitz, H., Weng, Z. and Zamore, P. D. (2010). Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43–56.CrossRefGoogle ScholarPubMed
Grant, W. N. (1994). Genetic variation in parasitic nematodes and its implications. International Journal for Parasitology 24, 821–830.CrossRefGoogle ScholarPubMed
Gray, N. K. and Hentze, M. W. (1994). Regulation of protein synthesis by mRNA structure. Molecular Biology Reports 19, 195–200.CrossRefGoogle ScholarPubMed
Gredell, J. A., Berger, A. K. and Walton, S. P. (2008). Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study. Biotechnology and Bioengineering 100, 744–755.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Gu, S., Jin, L., Zhang, F., Sarnow, P. and Kay, M. A. (2009). Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs. Nature Structural and Molecular Biology 16, 144–150.CrossRefGoogle Scholar
Hahn, P., Schmidt, C., Weber, M., Kang, J. and Bielke, W. (2004). RNA interference: PCR strategies for the quantification of stable degradation-fragments derived from siRNA-targeted mRNAs. Biomolecular Engineering 21, 113–117.CrossRefGoogle ScholarPubMed
Hamatake, M., Nishizawa, M., Yamamoto, N., Kato, S. and Sugiura, W. (2007). A simple competitive RT-PCR assay for quantitation of HIV-1 subtype B and non-B RNA in plasma. Journal of Virology Methods 142, 113–117.CrossRefGoogle ScholarPubMed
Heid, C. A., Stevens, J., Livak, K. J. and Williams, P. M. (1996). Real time quantitative PCR. Genome Research 6, 986–994.CrossRefGoogle ScholarPubMed
Higuchi, R., Fockler, C., Dollinger, G. and Watson, R. (1993). Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions. Biotechnology (N Y) 11, 1026–1030.Google ScholarPubMed
Holmes, K., Williams, C. M., Chapman, E. A. and Cross, M. J. (2010). Detection of siRNA induced mRNA silencing by RT-qPCR: considerations for experimental design. BMC Research Notes 3, 53.CrossRefGoogle ScholarPubMed
Hoerter, J. A. H., Krishnan, V., Lionberger, T. A. and Walter, N. G. (2011). siRNA-like double-stranded RNAs are specifically protected against degradation in human cell extract. PLoS ONE 6, e20359.CrossRefGoogle ScholarPubMed
Huang, G., Allen, R., Davis, E. L., Baum, T. J. and Hussey, R. S. (2006). Engineering broad root-knot resistance in transgenic plants by RNAi silencing of a conserved and essential root-knot nematode parasitism gene. Proceedings of the National Academy of Sciences, USA 103, 14302–14306.CrossRefGoogle ScholarPubMed
Huang, S. C., Chan, D. T., Smyth, D. J., Ball, G., Gounaris, K. and Selkirk, M. E. (2010). Activation of Nippostrongylus brasiliensis infective larvae is regulated by a pathway distinct from the hookworm Ancylostoma caninum. International Journal for Parasitology 40, 1619–1628.CrossRefGoogle ScholarPubMed
Huppi, K., Martin, S. E. and Caplen, N. J. (2005). Defining and assaying RNAi in mammalian cells. Molecular Cell 17, 1–10.CrossRefGoogle ScholarPubMed
Hutvagner, G. (2005). Small RNA asymmetry in RNAi: Function in RISC assembly and gene regulation. FEBS Letters 579, 5850–5857.CrossRefGoogle ScholarPubMed
Huvenne, H. and Smagghe, G. (2010). Mechanisms of dsRNA uptake in insects and potential of RNAi for pest control: A review. Journal of Insect Physiology 56, 227–235.CrossRefGoogle ScholarPubMed
Issa, Z., Grant, W. N., Stasiuk, S. and Shoemaker, C. B. (2005). Development of methods for RNA interference in the sheep gastrointestinal parasite, Trichostrongylus colubriformis. International Journal for Parasitology 35, 935–940.CrossRefGoogle ScholarPubMed
Jan, C. H., Friedman, R. C., Ruby, J. G. and Bartel, D. P. (2011). Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs. Nature 469, 97–101.CrossRefGoogle ScholarPubMed
Kamath, R. S. and Ahringer, J. (2003). Genome-wide RNAi screening in Caenorhabditis elegans. Methods 30, 313–321.CrossRefGoogle ScholarPubMed
Kamath, R. S., Fraser, A. G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, D. P., Zipperlen, P. and Ahringer, J. (2003). Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–237.CrossRefGoogle ScholarPubMed
Kikuchi, T., Cotton, J. A., Dalzell, J. J., Hasegawa, K., Kanzaki, N., McVeigh, P., Takanashi, T., Tsai, I. J., Assefa, S. A., Cock, P. J. A., Otto, T. D., Hunt, M., Reid, A. J., Sanchez-Flores, A., Tsuchihara, K., Larsson, M. C., Miwa, J., Maule, A. G., Sahashi, N., Jones, J. T. and Berriman, M. (2011). Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens 7(9), e1002219.CrossRefGoogle ScholarPubMed
Kim, D. H., Behlke, M. A., Rose, S. D., Chang, M. S., Choi, S. and Rossi, J. J. (2005). Synthetic dsRNA dicer substrates enhance RNAi potency and efficacy. Nature Biotechnology 23, 222–226.CrossRefGoogle ScholarPubMed
Kimber, M. J., Fleming, C. C., Prior, A., Jones, J. T., Halton, D. W. and Maule, A. G. (2002). Localisation of Globodera pallida FMRFamide-related peptide encoding genes using in situ hybridisation. International Journal for Parasitology 32, 1095–1105.CrossRefGoogle ScholarPubMed
Kimber, M. J., McKinney, S., McMaster, S., Day, T. A., Fleming, C. C. and Maule, A. G. (2007). Flp gene disruption in a parasitic nematode reveals motor dysfunction and unusual neuronal sensitivity to RNA interference. FASEB Journal 21, 1233–1243.CrossRefGoogle Scholar
Knight, M., Miller, A., Liu, Y., Scaria, P., Woodle, M. and Ittiprasert, W. (2011). Polyethyleneimine (PEI) mediated siRNA gene silencing in the Schistosoma mansoni snail host, Biomphalaria glabrata. PLoS Neglected Tropical Disease 5, e1212.CrossRefGoogle ScholarPubMed
Knox, D., Geldhof, P., Visser, A. and Britton, C. (2007). RNA interference in parasitic nematodes of animals: A reality check? Trends in Parasitology 23, 105–107.CrossRefGoogle ScholarPubMed
Kotze, A. C. and Bagnall, N. H. (2006). RNA interference in Haemonchus contortus: Suppression of beta-tubulin gene expression in L3, L4 and adult worms in vitro. Molecular and Biochemical Parasitology 145, 101–110.CrossRefGoogle ScholarPubMed
Krautz-Peterson, G., Bhardwaj, R., Faghiri, Z., Tararam, C. A. and Skelly, P. J. (2010a). RNA interference in schistosomes: Machinery and methodology. Parasitology 137, 485–495.CrossRefGoogle ScholarPubMed
Krautz-Peterson, G., Radwanska, M., Ndegwa, D., Shoemaker, C. B. and Skelly, P. J. (2007). Optimizing gene suppression in schistosomes using RNA interference. Molecular and Biochemical Parasitology 153, 194–202.CrossRefGoogle ScholarPubMed
Krautz-Peterson, G., Simoes, M., Faghiri, Z., Ndegwa, D., Oliveira, G., Shoemaker, C. B. and Skelly, P. J. (2010b). Suppressing glucose transporter gene expression in schistosomes impairs parasite feeding and decreases survival in the mammalian host. PLoS Pathogen 6, e1000932.CrossRefGoogle ScholarPubMed
Krautz-Peterson, G. and Skelly, P. J. (2008). Schistosoma mansoni: The dicer gene and its expression. Experimental Parasitology 118, 122–128.CrossRefGoogle ScholarPubMed
Le Jambre, L. F. (1993). Molecular variation in trichostrongylid nematodes from sheep and cattle. Acta Tropica 53, 331–343.CrossRefGoogle ScholarPubMed
Lendner, M., Doligalska, M., Lucius, R. and Hartmann, S. (2008). Attempts to establish RNA interference in the parasitic nematode Heligmosomoides polygyrus. Molecular and Biochemical Parasitology 161, 21–31.CrossRefGoogle ScholarPubMed
Li, L., Lin, X., Khvorova, A., Fesik, S. W. and Shen, Y. (2007). Defining the optimal parameters for hairpin-based knockdown constructs. RNA 13(10), 1765–1774.CrossRefGoogle ScholarPubMed
Lilley, C. J., Wang, D., Atkinson, H. J. and Urwin, P. E. (2011). Effective delivery of a nematode-repellent peptide using a root-cap-specific promoter. Plant Biotechnology Journal 9, 151–161.CrossRefGoogle ScholarPubMed
Lim, L. P., Lau, N. C., Garrett-Engele, P., Grimson, A., Schelter, J. M., Castle, J., Bartel, D. P., Linsley, P. S. and Johnson, J. M. (2005). Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773.CrossRefGoogle ScholarPubMed
Lipardi, C. and Paterson, B. M. (2010). Identification of an RNA-dependent RNA polymerase in Drosophila establishes a common theme in RNA silencing. Fly (Austin) 4, 30–35.CrossRefGoogle ScholarPubMed
Liu, F., Lu, J., Hu, W., Wang, S. Y., Cui, S. J., Chi, M., Yan, Q., Wang, X. R., Song, H. D., Xu, X. N., Wang, J. J., Zhang, X. L., Zhang, X., Wang, Z. Q., Xue, C. L., Brindley, P. J., McManus, D. P., Yang, P. Y., Feng, Z., Chen, Z. and Han, Z. G. (2006). New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum. PLoS Pathogen 2(4), e29.CrossRefGoogle ScholarPubMed
Louvet-Vallee, S., Kolotuev, I., Podbilewicz, B. and Felix, M. A. (2003). Control of vulval competence and centering in the nematode Oscheius sp. 1 CEW1. Genetics 163, 133–146.CrossRefGoogle ScholarPubMed
Lustigman, S., Zhang, J., Liu, J., Oksov, Y. and Hashmi, S. (2004). RNA interference targeting cathepsin L and Z-like cysteine proteases of Onchocerca volvulus confirmed their essential function during L3 molting. Molecular and Biochemical Parasitology 138, 165–170.CrossRefGoogle ScholarPubMed
Mannhalter, C., Koizar, D. and Mitterbauer, G. (2000). Evaluation of RNA isolation methods and reference genes for RT-PCR analyses of rare target RNA. Clinical Chemistry and Laboratory Medicine 38, 171–177.CrossRefGoogle ScholarPubMed
Mapes, C. J. (1969). The development of Haemonchus contortus in vitro. I. The effect of pH and pCO2 on the rate of development to the fourth-stage larva. Parasitology 59, 215–231.CrossRefGoogle Scholar
McGonigle, L., Mousley, A., Marks, N. J., Brennan, G. P., Dalton, J. P., Spithill, T. W., Day, T. A. and Maule, A. G. (2008). The silencing of cysteine proteases in Fasciola hepatica newly excysted juveniles using RNA interference reduces gut penetration. International Journal for Parasitology 38, 149–155.CrossRefGoogle ScholarPubMed
McVeigh, P., Mair, G. R., Novozhilova, E., Day, A., Zamanian, M., Marks, N. J., Kimber, M. J., Day, T. A. and Maule, A. G. (2011). Schistosome I/Lamides – A new family of bioactive helminth neuropeptides. International Journal for Parasitology 41, 905–913.CrossRefGoogle ScholarPubMed
Mizukami, C., Spiliotis, M., Gottstein, B., Yagi, K., Katakura, K. and Oku, Y. (2010). Gene silencing in Echinococcus multilocularis protoscoleces using RNA interference. Parasitology International 59, 647–652.CrossRefGoogle ScholarPubMed
Moffat, J., Reiling, J. and Sabatini, D. (2007). Off-target effects associated with long dsRNAs in Drosophila RNAi screens. Trends in Pharmacological Sciences 28, 149–151.CrossRefGoogle ScholarPubMed
Morales, M. E., Rinaldi, G., Gobert, G. N., Kines, K. J., Tort, J. F. and Brindley, P. J. (2008). RNA interference of Schistosoma mansoni cathepsin D, the apical enzyme of the hemoglobin proteolysis cascade. Molecular and Biochemical Parasitology 157, 160–168.CrossRefGoogle ScholarPubMed
Mourao, M. M., Dinguirard, N., Franco, G. R. and Yoshino, T. P. (2009). Phenotypic screen of early-developing larvae of the blood fluke, Schistosoma mansoni, using RNA interference. PLoS Neglected Tropical Disease 3, e502.CrossRefGoogle ScholarPubMed
Muthusamy, V., Bosenberg, M. and Wajapeyee, N. (2010). Redefining regulation of DNA methylation by RNA interference. Genomics 96, 191–198.CrossRefGoogle ScholarPubMed
Nabhan, J. F., El-Shehabi, F., Patocka, N. and Ribeiro, P. (2007). The 26S proteasome in Schistosoma mansoni: bioinformatic analysis, developmental expression, and RNA interference (RNAi) studies. Experimental Parasitology 117, 337–347.CrossRefGoogle ScholarPubMed
Nanda, J. C. and Stretton, A. O. (2010). In situ hybridization of neuropeptide-encoding transcripts afp-1, afp-3, and afp-4 in neurons of the nematode Ascaris suum. The Journal of Comparative Neurology 518, 896–910.CrossRefGoogle ScholarPubMed
Ni, J. Q., Zhou, R., Czech, B., Liu, L. P., Holderbaum, L., Yang-Zhou, D., Shim, H. S., Tao, R., Handler, D., Karpowicz, P., Binari, R., Booker, M., Brennecke, J., Perkins, L. A., Hannon, G. J. and Perrimon, N. (2011). A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nature Methods 8(5), 405–407.CrossRefGoogle ScholarPubMed
Nature Cell Biology Editorial (2003). Whither RNAi? Nature Cell Biology 5(6), 489–490.CrossRefGoogle Scholar
Nordgard, O., Kvaloy, J. T., Farmen, R. K. and Heikkila, R. (2006). Error propagation in relative real-time reverse transcription polymerase chain reaction quantification models: The balance between accuracy and precision. Analytical Biochemistry 356, 182–193.CrossRefGoogle ScholarPubMed
Nowotny, M., Gaidamakov, S. A., Crouch, R. J. and Yang, W. (2005). Crystal structures of RNase H bound to an RNA/DNA hybrid: Substrate specificity and metal-dependent catalysis. Cell 121, 1005–1016.CrossRefGoogle Scholar
Orban, T. I. and Izaurralde, E. (2005). Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA, 11, 459–469.CrossRefGoogle ScholarPubMed
Pak, J. and Fire, A. (2007). Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315, 241–244.CrossRefGoogle ScholarPubMed
Park, J. E., Lee, K. Y., Lee, S. J., Oh, W. S., Jeong, P. Y., Woo, T., Kim, C. B., Paik, Y. K. and Koo, H. S. (2008). The efficiency of RNA interference in Bursaphelenchus xylophilus. Molecules and Cells 26, 81–86.CrossRefGoogle ScholarPubMed
Park, B. J., Lee, D. G., Yu, J. R., Jung, S. K., Choi, K., Lee, J., Lee, J., Kim, Y. S., Lee, J. I., Kwon, J. Y., Lee, J., Singson, A., Song, W. K., Eom, S. H., Park, C. S., Kim, D. H., Bandyopadhyay, J. and Ahnn, J. (2001). Calreticulin, a calcium-binding molecular chaperone, is required for stress response and fertility in Caenorhabditis elegans. Molecular Biology of the Cell 12, 2835–2845.CrossRefGoogle ScholarPubMed
Pereira, T. C., Pascoal, V. D. B., Marchesini, R. B., Maia, I. G., Magalhães, L. A., Zanotti-Magalhães, E. M. and Lopes-Cendes, I. (2008). Schistosoma mansoni: Evaluation of an RNAi-based treatment targeting HGPRTase gene. Experimental Parasitology 118, 619–623.CrossRefGoogle ScholarPubMed
Pfaffl, M. W. (2001). A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research 29, e45.CrossRefGoogle ScholarPubMed
Pierson, L., Mousley, A., Devine, L., Marks, N. J., Day, T. A. and Maule, A. G. (2010). RNA interference in a cestode reveals specific silencing of selected highly expressed gene transcripts. International Journal for Parasitology 40, 605–615.CrossRefGoogle Scholar
Pires-daSilva, A. and Sommer, R. J. (2004). Conservation of the global sex determination gene tra-1 in distantly related nematodes. Genes and Development 18, 1198–1208.CrossRefGoogle ScholarPubMed
Pispa, J., Palmen, S., Holmberg, C. I. and Jantti, J. (2008). C. elegans dss-1 is functionally conserved and required for oogenesis and larval growth. BMC Developmental Biology 8, 51.CrossRefGoogle ScholarPubMed
Rosso, M. N., Jones, J. T. and Abad, P. (2009). RNAi and functional genomics in plant parasitic nematodes. Annual Reviews in Phytopathology 47, 207–232.CrossRefGoogle ScholarPubMed
Saleh, M. C., van Rij, R. P., Hekele, A., Gillis, A., Foley, E., O'Farrell, P. H. and Andino, R. (2006). The endocytic pathway mediates cell entry of dsRNA to induce RNAi silencing. Nature Cell Biology 8, 793–802.CrossRefGoogle ScholarPubMed
Samarasinghe, B., Knox, D. P. and Britton, C. (2010). Factors affecting susceptibility to RNA interference in Haemonchus contortus and in vivo silencing of an H11 aminopeptidase gene. International Journal for Parasitology 41, 51–59.CrossRefGoogle ScholarPubMed
Schubert, S., Grünweller, A., Erdmann, V. and Kurreck, J. (2005). Local RNA target structure influences siRNA efficacy: Systematic analysis of intentionally designed binding regions. Journal of Molecular Biology 348, 883–893.CrossRefGoogle ScholarPubMed
Schultz, N., Marenstein, D. R., De Angelis, D. A., Wang, W. Q., Nelander, S., Jacobsen, A., Marks, D. S., Massague, J. and Sander, C. (2011). Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-beta pathway and reveal microRNA regulation of TGFBR2. Silence 2, 3.CrossRefGoogle ScholarPubMed
Seinen, E., Burgerhof, J. G., Jansen, R. C. and Sibon, O. C. (2010). RNAi experiments in D. melanogaster: Solutions to the overlooked problem of off-targets shared by independent dsRNAs. PLoS One 5, e13119.CrossRefGoogle Scholar
Seinen, E., Burgerhof, J. G., Jansen, R. C. and Sibon, O. C. (2011). RNAi-induced off-target effects in Drosophila melanogaster: frequencies and solutions. Briefings in Functional Genomics 10, 206–214.CrossRefGoogle ScholarPubMed
Senthil-Kumar, M. and Mysore, K. S. (2011). Caveat of RNAi in plants: the off-target effect. Methods in Molecular Biology 744, 13–25.CrossRefGoogle ScholarPubMed
Shao, Y., Chan, C. Y., Maliyekkel, A., Lawrence, C. E., Roninson, I. B. and Ding, Y. (2007). Effect of target secondary structure on RNAi efficiency. RNA 13, 1631–1640.CrossRefGoogle ScholarPubMed
Shepard, A. R., Jacobson, N. and Clark, A. F. (2005). Importance of quantitative PCR primer location for short interfering RNA efficacy determination. Annals of Biochemistry 344, 287–288.CrossRefGoogle ScholarPubMed
Shih, J. D., Fitzgerald, M. C., Sutherlin, M. and Hunter, C. P. (2009). The SID-1 double-stranded RNA transporter is not selective for dsRNA length. RNA 15, 384–390.CrossRefGoogle Scholar
Shih, J. D. and Hunter, C. P. (2011). SID-1 is a dsRNA-selective dsRNA-gated channel. RNA 17, 1057–1065.CrossRefGoogle ScholarPubMed
Shingles, J., Lilley, C. J., Atkinson, H. J. and Urwin, P. E. (2007). Meloidogyne incognita: Molecular and biochemical characterisation of a cathepsin L cysteine proteinase and the effect on parasitism following RNAi. Experimental Parasitology 115, 114–120.CrossRefGoogle ScholarPubMed
Sijen, T., Steiner, F. A., Thijssen, K. L. and Plasterk, R. H. (2007). Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315, 244–247.CrossRefGoogle Scholar
Siomi, H. and Siomi, M. C. (2009). On the road to reading the RNA-interference code. Nature 457, 396–404.CrossRefGoogle ScholarPubMed
Sithigorngul, P., Jarecki, J. L. and Stretton, A. O. (2011). A specific antibody to neuropeptide AF1 (KNEFIRFamide) recognizes a small subset of neurons in Ascaris suum: Differences from Caenorhabditis elegans. Journal of Comparative Neurology 519, 1546–1561.CrossRefGoogle ScholarPubMed
Snove, O. Jr. and Rossi, J. J. (2006). Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi. Genome Biology 7, 231.CrossRefGoogle ScholarPubMed
Sommerville, R. I. (1966). The development of Haemonchus contortus to the fourth stage in vitro. Journal of Parasitology 52, 127–136.CrossRefGoogle Scholar
Song, C., Gallup, J. M., Day, T. A., Bartholomay, L. C. and Kimber, M. J. (2010). Development of an in vivo RNAi protocol to investigate gene function in the filarial nematode, Brugia malayi. PLoS Pathogens 6, e1001239.CrossRefGoogle Scholar
Song, E., Zhu, P., Lee, S. K., Chowdhury, D., Kussman, S., Dykxhoorn, D. M., Feng, Y., Palliser, D., Weiner, D. B., Shankar, P., Marasco, W. A. and Lieberman, J. (2005). Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors. Nature Biotechnology 23, 709–717.CrossRefGoogle ScholarPubMed
Souret, F. F., Kastenmayer, J. P. and Green, P. J. (2004). AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Molecular Cell 23, 173–183.CrossRefGoogle Scholar
Stefanic, S., Dvorak, J., Horn, M., Braschi, S., Sojka, D., Ruelas, D. S., Suzuki, B., Lim, K. C., Hopkins, S. D., McKerrow, J. H. and Caffrey, C. R. (2010). RNA interference in Schistosoma mansoni schistosomula: Selectivity, sensitivity and operation for larger-scale screening. PLoS Neglected Tropical Disease 4, e850.CrossRefGoogle ScholarPubMed
Subramanya, S., Kim, S. S., Manjunath, N. and Shankar, P. (2010). RNA interference-based therapeutics for human immunodeficiency virus HIV-1 treatment: synthetic siRNA or vector-based shRNA? Expert Opinion on Biological Therapy 10, 201–213.CrossRefGoogle ScholarPubMed
Surzhik, M. A., Duks, A. E., Diatlova, N. G., Glazunov, E. A., Feldmane, G. I. and Timkovskii, A. L. (1993). Interrelationship between the chain length of poly-L-lysine and the degree of protection of polyribonucleotide interferon inducers from human blood nucleases. Antibiotiki Khimioterapiya 38, 21–25.Google ScholarPubMed
Terenius, O., Papanicolaou, A., Garbutt, J. S., Eleftherianos, I., Huvenne, H., Kanginakudru, S., Albrechtsen, M., An, C., Aymeric, J. L., Barthel, A., Bebas, P., Bitra, K., Bravo, A., Chevalier, F., Collinge, D. P., Crava, C. M., de Maagd, R. A., Duvic, B., Erlandson, M., Faye, I., Felfoldi, G., Fujiwara, H., Futahashi, R., Gandhe, A. S., Gatehouse, H. S., Gatehouse, L. N., Giebultowicz, J. M., Gomez, I., Grimmelikhuijzen, C. J., Groot, A. T., Hauser, F., Heckel, D. G., Hegedus, D. D., Hrycaj, S., Huang, L., Hull, J. J., Iatrou, K., Iga, M., Kanost, M. R., Kotwica, J., Li, C., Li, J., Liu, J., Lundmark, M., Matsumoto, S., Meyering-Vos, M., Millichap, P. J., Monteiro, A., Mrinal, N., Niimi, T., Nowara, D., Ohnishi, A., Oostra, V., Ozaki, K., Papakonstantinou, M., Popadic, A., Rajam, M. V., Saenko, S., Simpson, R. M., Soberon, M., Strand, M. R., Tomita, S., Toprak, U., Wang, P., Wee, C. W., Whyard, S., Zhang, W., Nagaraju, J., Ffrench-Constant, R. H., Herrero, S., Gordon, K., Swevers, L. and Smagghe, G. (2011). RNA interference in Lepidoptera: an overview of successful and unsuccessful studies and implications for experimental design. Journal of Insect Physiology 57, 231–245.CrossRefGoogle ScholarPubMed
Terrazas, M. and Kool, E. T. (2009). RNA major groove modifications improve siRNA stability and biological activity. Nucleic Acids Research 37, 346–353.CrossRefGoogle ScholarPubMed
Timmons, L., Court, D. L. and Fire, A. (2001). Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263, 103–112.CrossRefGoogle ScholarPubMed
Tomari, Y., Matranga, C., Haley, B., Martinez, N. and Zamore, P. D. (2004). A protein sensor for siRNA asymmetry. Science 306, 1377–1380.CrossRefGoogle ScholarPubMed
Tomoyasu, Y., Miller, S. C., Tomita, S., Schoppmeier, M., Grossmann, D. and Bucher, G. (2008). Exploring systemic RNA interference in insects: A genome-wide survey for RNAi genes in Tribolium. Genome Biology 9, R10.CrossRefGoogle ScholarPubMed
Ulvila, J., Parikka, M., Kleino, A., Sormunen, R., Ezekowitz, R. A., Kocks, C. and Ramet, M. (2006). Double-stranded RNA is internalized by scavenger receptor-mediated endocytosis in Drosophila S2 cells. Journal of Biological Chemistry 281, 14370–14375.CrossRefGoogle ScholarPubMed
Urwin, P. E., Lilley, C. J. and Atkinson, H. J. (2002). Ingestion of double-stranded RNA by preparasitic juvenile cyst nematodes leads to RNA interference. Molecular Plant Microbe Interactions 15, 747–752.CrossRefGoogle ScholarPubMed
Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A. and Speleman, F. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 3, RESEARCH0034.CrossRefGoogle ScholarPubMed
Viney, M. E. and Thompson, F. J. (2006). Two hypotheses to explain why RNA interference does not work in animal parasitic nematodes. International Journal for Parasitology 38, 43–47.CrossRefGoogle Scholar
Visser, A., Geldhof, P., de Maere, V., Knox, D. P., Vercruysse, J. and Claerebout, E. (2006). Efficacy and specificity of RNA interference in larval life-stages of Ostertagia ostertagi. Parasitology 133, 777–783.CrossRefGoogle ScholarPubMed
Wong, M. L. and Medrano, J. F. (2005). Real-time PCR for mRNA quantitation. BioTechniques 39, 75–85.CrossRefGoogle ScholarPubMed
Xu, K., Tavernarakis, N. and Driscoll, M. (2001). Necrotic cell death in C. elegans requires the function of calreticulin and regulators of Ca2+ release from the endoplasmic reticulum. Neuron 31, 957–971.CrossRefGoogle Scholar
Yadav, B., Veluthambi, K. and Subramaniam, K. (2006). Host-generated double stranded RNA induces RNAi in plant-parasitic nematodes and protects the host from infection. Molecular and Biochemical Parasitology 148, 219–222.CrossRefGoogle ScholarPubMed
Zhao, Z., Lei, L., Liu, M., Zhu, S., Ren, C., Wang, X. and Shen, J. (2008). Schistosoma japonicum: Inhibition of mago nashi gene expression by shRNA-mediated RNA interference. Experimental Parasitology 119, 379–384.CrossRefGoogle ScholarPubMed
Zhuang, J. J. and Hunter, C. P. (2011). Tissue specificity of Caenorhabditis elegans enhanced RNA interference mutants. Genetics 188, 235–237.CrossRefGoogle ScholarPubMed
Zisoulis, D. G., Lovci, M. T., Wilbert, M. L., Hutt, K. R., Liang, T. Y., Pasquinelli, A. E. and Yeo, G. W. (2010). Comprehensive discovery of endogenous argonaute binding sites in Caenorhabditis elegans. Nature Structural and Molecular Biology 17, 173–179.CrossRefGoogle ScholarPubMed
Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31, 3406–3415.CrossRefGoogle ScholarPubMed