THE IMPACT OF siRNA FEATURES ON ITS FIDELITY AND EF- FICIENCY IN TARGETING SOLUBLE ACID INVERTASE GENE IN SUGARCANE

Authors

  • SHEREEN K. M. KHALED Sugar Crop Research Institute (SCRI), Agriculture Research Center
  • F. M. ABDEL-TAWAB Genetics Department, Faculty of Agriculture, Ain-Shams University
  • EMAN M. FAHMY Genetics Department, Faculty of Agriculture, Ain-Shams University
  • E. M. AHMED Sugar Crop Research Institute (SCRI), Agriculture Research Center
  • KH. A. KHALED Genetics Department, Faculty of Agriculture, Beni-suef University

Abstract

Bioinformatic tools to design a suitable siRNA are an essential step before conducting any laboratory experiment. The identification of highly active siRNA is the corner stone in any silencing application. Five separate steps were used in these studies to test the siRNA efficacy in-silico to evaluate the validation of the siRNA sequence targeting soluble acid invertase gene in sugarcane. The used programs and websites for designing siRNA molecule to silence SAI gene in sugarcane confirmed their validity in designing an efficient, less laboring and accurate siRNA sequence. The subsequent five steps were essential to avoid any side effect on the overall physiological pattern in the plant.

References

Bart, Rebecca, M. Chern, C. Park, Laura Bartley and Pamela C. Ronald (2006). A novel system for gene silencing using siRNAs in rice leaf and stem-derived protoplasts. Plant Methods, 2: 13-17.

Bernstein, E., A. A. Caudy, S. M. Hammond and G. J. Hannon (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409: 363-366.

Elbashir, S. M., W. Lendeckel and T. Tuschl (2001). RNA interference is mediated by 21- and 22- nucleotide RNAs. Genes Dev., 15: 188-200.

Guimaraȅs, Claudia T., G. R. Sills and B. W. S. Sobral (1997). Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. Proc. Natl. Acad. Sci. USA, 94: 14261-14266.

Hamilton, A. J. and D. C. Baulcombe (1999). A novel species of small anti-sense RNA in posttranscriptional gene silencing. Science, 286: 950-952.

Holen, T., M. Amarzguioui, M. T. Wiiger, E. Babaie and H. Prydz (2002). Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Research, 30: 1757-1766.

Kamthan, A., A. Chaudhuri, M. Kamthan and A. Datta (2015). Small RNAs in plants: recent development and application for crop improvement. Front. Plant Sci., 6: 208-212.

Khaled, Shereen K. M., F. M. Abdel-Tawab, Eman M. Fahmy, E. A. M. Amer and K. A. Khaled (2018). The siRNA efficacy of soluble acid invertase down-regulation in Sugarcane (Saccharum spp.). Arab Univ. J. Agri. Sci., Special issue, 26(2).

Kumar, P., M. Kamle and A. Pandey (2012). RNAi: new era of functional genomics for crop improvement. In: Goyal A, Maheshwari P(ed) Frontiers on recent developments in plant science, Bentham Sci., 1: 24-38.

Lingle, Sarah E. (1999). Sugar metabolism during growth and development in sugarcane internodes. Crop Sci., 39: 480-486.

Luo, K. Q. and D. C. Chang (2004). The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region. Biochemical and Biophysical Research Communications, 318: 303-310.

Mayavan, S., K. Subramanyam, B. Jaganath, D. Sathish, M. Manickavasagam and A. Ganapathi (2015). Agrobacterium-mediated in-planta genetic transformation of sugarcane setts. Plant Cell Rep., 34: 1835-1848.

Patzel, V., S. Rutz, I. Dietrich, C. Koberle, A. Scheffold and She Kaufmann (2005). Design of siRNA producing unstructured guide RNAs results in improved RNA interference efficiency. Nature Biotechnology, 23: 1440-1444.

Prathima, P. T., T. V. Suparna, S. Anishma, R. Punnya and K. Ramalakshmi (2014). Cloning and characterization of a differentially regulated invertase inhibitor gene during sucrose accumulation in Sugarcane. Journal of Sugarcane Research, 4: 21-28.

Pascut, D., G. Bedogni and C. Tiribelli (2015). Silencing efficacy prediction: a retrospective study on target mRNA features. Bioscience Reports, 35-42.

Schwarz, D. S., G. Hutvágner, T. Du, Z. Xu, N. Aronin and P. D. Zamore (2003). Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115: 199-208.

Sunkar, R. and J. K. Zhu (2007). Micro RNAs and Short-interferring RNAs in plants. J. Integrative Plant Biology, 49: 817-826.

Tuschl, T. (2001). RNA interference and small interfering RNAs. Chem. Biochem., 2: 239-145.

Wang, J., B. Roe, S. Macmil, Q. Yu, J. E. Murray, H. Tang, C. Chen, F. Najar, G. Wiley, J. Bowers, Marie-Anne Van Sluys, D. S. Rokhsar, M. E. Hudson, S. P. Moose, A. H. Paterson and R. Ming (2010). Micro-collinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics, 11: 261-278.

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2019-04-13

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