AmiRNA Designer - new method of artificial miRNA design

• Authors: Agnieszka Mickiewicz , Agnieszka Rybarczyk , Joanna Sarzynska , Marek Figlerowicz , Jacek Blazewicz
• Languages of publication: EN

Abstracts

EN

MicroRNAs (miRNAs) are small non-coding RNAs that have been found in most of the eukaryotic organisms. They are involved in the regulation of gene expression at the post-transcriptional level in a sequence specific manner. MiRNAs are produced from their precursors by Dicer-dependent small RNA biogenesis pathway. Involvement of miRNAs in a wide range of biological processes makes them excellent candidates for studying gene function or for therapeutic applications. For this purpose, different RNA-based gene silencing techniques have been developed. Artificially transformed miRNAs (amiRNAs) targeting one or several genes of interest represent one of such techniques being a potential tool in functional genomics. Here, we present a new approach to amiRNA*design, implemented as AmiRNA Designer software. Our method is based on the thermodynamic analysis of the native miRNA/miRNA* and miRNA/target duplexes. In contrast to the available automated tools, our program allows the user to perform analysis of natural miRNAs for the organism of interest and to create customized constraints for the design stage. It also provides filtering of the amiRNA candidates for the potential off-targets. AmiRNA Designer is freely available at http://www.cs.put.poznan.pl/arybarczyk/AmiRNA/.

Keywords

EN

artificial miRNA; RNAi; gene regulation; sequence specific; thermodynamic profiles

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2016
• Volume: 63
• Issue: 1
• Pages: 71-77

Dates

published

2016

received

2015-02-09

revised

2015-09-01

accepted

2016-01-06

(unknown)

2016-01-19

Contributors

author

Agnieszka Mickiewicz

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Agnieszka Rybarczyk

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
• Institute of Computing Science, Poznan University of Technology, Poznań, Poland

author

Joanna Sarzynska

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Marek Figlerowicz

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
• Institute of Computing Science, Poznan University of Technology, Poznań, Poland

author

Jacek Blazewicz

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
• Institute of Computing Science, Poznan University of Technology, Poznań, Poland

References

• Axtell MJ, Westholm JO, Lai EC (2011) Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biology 12: 221.
• Baby J, Vrundha N, Chandy S (2012) AmiRzyn: PERL Centered Artificial MicroRNA Designing Aid. Int Res J Biol Sci 1: 18-23.
• Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
• Blazewicz J, Figlerowicz M, Kasprzak M, Nowacka M, Rybarczyk A (2011) RNA partial degradation problem: motivation, complexity, algorithm. J Comp Biol 18: 821-834.
• Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik JF (2013) Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Res 23: 1675-1689.
• Brodersen P, Voinnet O (2009) Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 10: 141-148.
• Carbonell A, Takeda A, Fahlgren N, Johnson SC, Cuperus JT, Carrington JC (2014) New generation of artificial microRNA and synthetic trans-acting small interfering RNA vectors for efficient gene silencing in Arabidopsis. Plant Physiol 165: 15-29.
• Carthew RW, Sontheimer EJ (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
• Chau BL, Lee KA (2007) Function and anatomy of plant siRNA pools derived from hairpin transgenes. Plant Methods 3: 13.
• Chekulaeva M, Filipowicz W (2009) Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Curr Opin Cell Biol 21: 452-460.
• Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39: W155-W159.
• Dong Q, Schlueter SD, Brendel V (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Res 32: D354-D359.
• Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 36: D959-D965.
• Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM (2009) The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA 15: 2219-2235.
• Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
• Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158.
• Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD (2005) ASRP: the Arabidopsis small RNA project database. Nucleic Acids Res 33: D637-D640.
• Fahlgren N, Hill ST, Carrington JC, Carbonell A (2015) P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA. Bioinformatics 32: 157-158.
• Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125: 887-901.
• Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216.
• Kim JY, Kwak KJ, Jung HJ, Lee HJ, Kang H (2010) MicroRNA402 affects seed germination of Arabidopsis thaliana under stress conditions via targeting DEMETER-LIKE Protein3 mRNA. Plant Cell Physiol 51: 1079-1083.
• Kim VN (2005a) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6: 376-385.
• Kim VN (2005b) Small RNAs: classification, biogenesis, and function. Mol Cells 19: 1-15.
• Krol J, Sobczak K, Wilczynska U, Drath M, Jasinska A, Kaczynska D, Krzyzosiak WJ (2004) Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem 279: 42230-42239.
• Kurihara Y, Watanabe Y (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA 101: 12753-12758.
• Laganà A, Acunzo M, Romano G, Pulvirenti A, Veneziano D, Cascione L, Giugno R, Gasparini P, Shasha D, Ferro A, Croce CM (2014) miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs. Nucleic Acids Res 42: 5416-5425.
• Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
• Li JF, Chung HS, Niu Y, Bush J, McCormack M, Sheen J (2013) Comprehensive protein-based artificial microRNA screens for effective gene silencing in plants. Plant Cell 25: 1507-1522.
• Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991-1008.
• Mallory AC, Vaucheret H (2004) MicroRNAs: something important between the genes. Curr Opin Plant Biol 7: 120-125.
• Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. EMBO J 23: 3356-3364.
• Markham NR, Zuker M (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol 453: 3-31.
• Meola N, Gennarino VA, Banfi S (2009) microRNAs and genetic diseases. Pathogenetics 2: 7.
• Nowacka M, Jackowiak P, Rybarczyk A, Magacz T, Strozycki PM, Barciszewski J, Figlerowicz M (2012) 2D-PAGE as an effective method of RNA degradome analysis. Mol Biol Rep 39: 139-146.
• Obernosterer G, Meister G, Poy MN, Kuras A (2006) The impact of small RNAs. Microsymposium on Small RNAs. EMBO Rep 8: 23-27.
• Ossowski S, Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 53: 674-690.
• Petri S, Meister G (2013) siRNA design principles and off-target effects. Methods Mol Biol 986: 59-71.
• Rybarczyk A, Szostak N, Antczak M, Zok T, Popenda M, Adamiak R, Blazewicz J, Szachniuk M (2015) New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinformatics 16: 276.
• Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 1121-1133.
• Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17: 196-203.
• Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001-2019.
• Szostak N, Royo F, Rybarczyk A, Szachniuk M, Blazewicz J, del Sol A, Falcon-Perez JM (2014) Sorting signal targeting mRNA into hepatic extracellular vesicles. RNA Biol 11: 836-844.
• Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20: 515-24.
• Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci 91: 9218-9222.
• Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol 138: 2145-2154.
• Yu S, Pilot G (2014) Testing the efficiency of plant artificial microRNAs by transient expression in Nicotiana benthamiana reveals additional action at the translational level. Front Plant Sci 5: 622.

Identifiers

DOI

10.18388/abp.2015_989