New Algorithm for Analysis of Off-target Effects in siRNA Screens

Karol Kozak, Sandra Kaestner, Thomas Wild, Andreas Vonderheit, Benjamin Misselwitz, Ulrike Kutay, Gabor Csucs

Abstract

The occurrence of RNAi side effects called “off-target effects” is still a challenging aspect in the interpretation of data from large-scale RNA interference screens. To reduce off-target effects, improved algorithms have been developed for small interfering RNA (siRNA) design, but also chemical modifications of double stranded RNA molecules were introduced by the various commercial providers. To aid the analysis of large-scale screens, we present a new algorithm and tool for the prediction of potential off-target effects that can be applied to RNAi experimental data. Our approach provides different possibilities to search for homologies between individual siRNAs of cellular mRNAs. We demonstrate our approach on a ribosomal RNAi screening dataset.

References

  1. Alemán, L. M., Doench, J. G. and Sharp, P. A., 2007. Comparison of sirna-induced off-target rna and protein effects. RNA, 13(3):385-95.
  2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W and Lipman, D. J., 1990. Basic local alignment search tool. J Mol Biol, 215(3):403-10.
  3. Amarzguioui, M., Holen,T., Babaie, E. and Prydz, H. 2003. Tolerance for mutations and chemical modifications in a sirna. Nucleic Acids Res, 31(2):589-95.
  4. Anderson, E. M., Birmingham, A., Baskerville, S., Reynolds, A., Maksimova, E., Leake, D., Fedorov, Y., Karpilow, J. and Khvorova, A., 2008. Experimental validation of the importance of seed complement frequency to sirna specificity. RNA, 14(5):853-61.
  5. Birmingham, A., Anderson, E. M., Reynolds, A., IlsleyTyree, D., Leake, D., Fedorov, Y., Baskerville, S., Maksimova, E., Robinson, K., Karpilow, J., Marshall, W.S and Khvorova, A., 2006. 378 utr seed matches, but not overall identity, are associated with rnai offtargets. Nat Methods, 3(3):199-204.
  6. Doench, J. G., Petersen, C. P. and Sharp, P. A., 2003. Sirnas can function as mirnas. Genes Dev, 17(4):438- 42.
  7. 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 J, 20(23):6877-88.
  8. Fedorov, Y., King, A., Anderson, E. M., Karpilow, J., Ilsley, D., Marshall, W. S. and Khvorova, A., 2005. Different delivery methods-different expression profiles. Nat Methods, 2(4):241.
  9. 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(7):1188- 96.
  10. Grillo, G., Turi, A., Licciulli, F., Mignone, F., Liuni, S., Banfi, S., Gennarino, V. A., Horner, D. S., Pavesi, G., Picardi, E., Pesole, G., 2010. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res., 38, 75-80.
  11. Hannon, H. J., 2002. Rna interference. Nature, 418(6894):244-51, July.
  12. Haley, B. and Zamore, P. D., 2004. Kinetic analysis of the rnai enzyme complex. Nat Struct Mol Biol, 11(7):599- 606.
  13. HCDC web page, bioinformatics module: [http://hcdc.ethz.ch/index.php?view=article&id=25] Jackson, A. L, Burchard, J., Leake,D., Reynolds, A., Schelter, J., Guo, J., Johnson, J. M., Lim, L., Karpilow, J., Nichols, K., Marshall, W. S., Khvorova, A. and Linsley, P. S., 2006. Position-specific chemical modification of sirnas reduces "off-target" transcript silencing. RNA, 12(7):1197-205.
  14. Jackson, A. L., Burchard, J., Schelter, J., Chau, B. N., Cleary, M., Lim, L. and Linsley, P. S., 2006. Widespread sirna "off-target" transcript silencing mediated by seed region sequence complementarity. RNA, 12(7):1179-87.
  15. 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(6):635-7.
  16. Lewis, B. P., Burge, C. B. and Bartel, D. P., 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microrna targets. Cell, 120(1):15-20.
  17. Lin, X., Ruan, X., Anderson, M. G., McDowell, J. A., Kroeger, P. E., Fesik, S. W. and Shen, Y., 2005. Sirnamediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res, 33(14):4527-35.
  18. Saxena, S., Jónsson, Z.O. and Dutta, A. 2003. Small rnas with imperfect match to endogenous mrna repress translation. implications for off-target activity of small inhibitory rna in mammalian cells. J Biol Chem, 278(45):44312-9.
  19. Semizarov, D., Frost, L., Sarthy, A., Kroeger, P.A, Halbert, D. N. and Fesik, S. W., 2005. Specificity of short interfering rna determined through gene expression signatures. Proc Natl Acad Sci U S A, 100(11):6347-52.
  20. Smith, T. F. and Waterman, M. S., 1981. Identification of common molecular subsequences. J Mol Biol, 147(1):195-7.
  21. Ui-Tei, K., Naito, Y., Nishi, K., Juni, A. and Saigo, K., 2008. Thermodynamic stability and watson-crick base pairing in the seed duplex are major determinants of the efficiency of the sirna-based off-target effect. Nucleic Acids Res, 36(22):7100-9.
  22. Wild, T., Horvath, P., Wyler, E., Widmann, B., Badertscher, L., Zemp, I., Kozak, K., Csusc, G., Lund, E., Kutay, U., (2010) A protein inventory of human ribosome biogenesis reveals an essential function of Exportin 5 in 60S subunit export. PLoS Biol, 8:e1000522.
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Paper Citation


in Harvard Style

Kozak K., Kaestner S., Wild T., Vonderheit A., Misselwitz B., Kutay U. and Csucs G. (2013). New Algorithm for Analysis of Off-target Effects in siRNA Screens . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 253-260. DOI: 10.5220/0004185802530260


in Bibtex Style

@conference{bioinformatics13,
author={Karol Kozak and Sandra Kaestner and Thomas Wild and Andreas Vonderheit and Benjamin Misselwitz and Ulrike Kutay and Gabor Csucs},
title={New Algorithm for Analysis of Off-target Effects in siRNA Screens},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={253-260},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004185802530260},
isbn={978-989-8565-35-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - New Algorithm for Analysis of Off-target Effects in siRNA Screens
SN - 978-989-8565-35-8
AU - Kozak K.
AU - Kaestner S.
AU - Wild T.
AU - Vonderheit A.
AU - Misselwitz B.
AU - Kutay U.
AU - Csucs G.
PY - 2013
SP - 253
EP - 260
DO - 10.5220/0004185802530260