Antisense oligonucleotide technology as a research tool in plant biology
Anna Wdowikowska
A and Malgorzata Janicka A *
+ Author Affiliations
- Author Affiliations
A Department of Plant Molecular Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland.
Functional Plant Biology 49(1) 1-12 https://doi.org/10.1071/FP21194
Submitted: 4 August 2021 Accepted: 20 October 2021 Published: 19 November 2021
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
An antisense oligonucleotide (ASO) is a short single-stranded deoxyribonucleotide complementary to the sense strand of a selected nucleic acid. As a result, an ASO can modulate gene expression through several mechanisms. The technology based on ASO has already been applied in studies on gene function in mammalian cells and selective therapeutic strategies for many diseases. The conceptual simplicity and low cost of this method, and the developments in the field of plant genome sequencing observed in the last decades, have paved the way for the ASO method also in plant biology. It is applied in gene function analysis as well as the development of non-invasive plant production technology involving gene modifications without transgenesis. Therefore, the first part of this review provides a comprehensive overview of the structure, mechanism of action and delivery methods of ASOs in plants and shows the most important features essential for the proper design of individual experiments. We also discuss potential issues and difficulties that may arise during practical ASO implementation. The second part of this article contains an analysis of ASO applications in various studies in the field of plant biology. We presented for the first time that ASOs were also successfully applied in cucumber.
Keywords: antisense, ASO application, ASO technology, cucumber, gene function, modification of gene expression, oligonucleotide, plant biology studies.
References
Baker BF, Lot SS, Condon TP, Cheng-Flournoy S, Lesnik EA, Sasmor HM, Bennett CF (1997) 2′-O-(2-Methoxy) ethyl-modified anti-intercellular adhesion molecule 1 (ICAM-1) oligonucleotides selectively increase the ICAM-1 mRNA level and inhibit formation of the ICAM-1 translation initiation complex in human umbilical vein endothelial cells. Journal of Biological Chemistry 272, 11994–12000.| 2′-O-(2-Methoxy) ethyl-modified anti-intercellular adhesion molecule 1 (ICAM-1) oligonucleotides selectively increase the ICAM-1 mRNA level and inhibit formation of the ICAM-1 translation initiation complex in human umbilical vein endothelial cells.Crossref | GoogleScholarGoogle Scholar |
Bennett CF, Cowsert LM (1999) Antisense oligonucleotides as a tool for gene functionalization and target validation. Biochimica et Biophysica Acta (BBA) – Gene Structure and Expression 1489, 19–30.
| Antisense oligonucleotides as a tool for gene functionalization and target validation.Crossref | GoogleScholarGoogle Scholar |
Chan JHP, Lim S, Wong WSF (2006) Antisense oligonucleotides: from design to therapeutic application. Clinical and Experimental Pharmacology and Physiology 33, 533–540.
| Antisense oligonucleotides: from design to therapeutic application.Crossref | GoogleScholarGoogle Scholar |
Chiriboga CA, Swoboda KJ, Darras BT, Iannaccone ST, Montes J, De Vivo DC, Norris DA, Bennett CF, Bishop KM (2016) Results from a phase 1 study of nusinersen (ISIS-SMN(Rx)) in children with spinal muscular atrophy. Neurology 86, 890–897.
| Results from a phase 1 study of nusinersen (ISIS-SMN(Rx)) in children with spinal muscular atrophy.Crossref | GoogleScholarGoogle Scholar | 26865511PubMed |
Crooke ST (2000) Progress in antisense technology: the end of the beginning. Methods in Enzymology 313, 3–45.
| Progress in antisense technology: the end of the beginning.Crossref | GoogleScholarGoogle Scholar | 10595347PubMed |
Crooke ST (2017) Molecular mechanisms of antisense oligonucleotides. Nucleic Acid Therapeutics 27, 70–77.
| Molecular mechanisms of antisense oligonucleotides.Crossref | GoogleScholarGoogle Scholar | 28080221PubMed |
Crooke ST, Wang S, Vickers TA, Shen W, Liang XH (2017) Cellular uptake and trafficking of antisense oligonucleotides. Nature Biotechnology 35, 230–237.
| Cellular uptake and trafficking of antisense oligonucleotides.Crossref | GoogleScholarGoogle Scholar | 28244996PubMed |
PNA Bio Inc (2021) Custom PNA oligonucleotide synthesis. Available at http://panagene.com. [Accessed 1 July 2021]
Dias N, Stein CA (2002) Antisense oligonucleotides: basic concepts and mechanisms. Molecular Cancer Therapeutics 1, 347–355.
Dinç E, Tóth SZ, Schansker G, Ayaydin F, Kovács L, Dudits D, Garab G, Bottka S (2011) Synthetic antisense oligodeoxynucleotides to transiently suppress different nucleus- and chloroplast-encoded proteins of higher plant chloroplasts. Plant Physiology 157, 1628–1641.
| Synthetic antisense oligodeoxynucleotides to transiently suppress different nucleus- and chloroplast-encoded proteins of higher plant chloroplasts.Crossref | GoogleScholarGoogle Scholar | 21980174PubMed |
Ding Y, Chan CY, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Research 32, W135–W141.
| Sfold web server for statistical folding and rational design of nucleic acids.Crossref | GoogleScholarGoogle Scholar | 15215366PubMed |
Dzialo M, Szopa J, Czuj T, Zuk M (2017) Oligodeoxynucleotides can transiently up- and downregulate CHS gene expression in flax by changing DNA methylation in a sequence-specific manner. Frontiers in Plant Science 8, 755
| Oligodeoxynucleotides can transiently up- and downregulate CHS gene expression in flax by changing DNA methylation in a sequence-specific manner.Crossref | GoogleScholarGoogle Scholar | 28555142PubMed |
Dzialo M, Szopa J, Hnitecka A, Zuk M (2019) Transgenerational perpetuation of CHS gene expression and dna methylation status induced by short oligodeoxynucleotides in flax (Linum usitatissimum. International Journal of Molecular Science 20, 3983
| Transgenerational perpetuation of CHS gene expression and dna methylation status induced by short oligodeoxynucleotides in flax (Linum usitatissimum.Crossref | GoogleScholarGoogle Scholar |
Estruch JJ, Kadwell S, Merlin E, Crossland L (1994) Cloning and characterization of a maize pollen-specific calcium-dependent calmodulin-independent protein kinase. Proceedings of the National Academy of Sciences 91, 8837–8841.
| Cloning and characterization of a maize pollen-specific calcium-dependent calmodulin-independent protein kinase.Crossref | GoogleScholarGoogle Scholar |
Goyal N, Narayanaswami P (2018) Making sense of antisense oligonucleotides: a narrative review. Muscle & Nerve 57, 356–370.
| Making sense of antisense oligonucleotides: a narrative review.Crossref | GoogleScholarGoogle Scholar |
Gupta A, Mishra A, Puri N (2017) Peptide nucleic acids: advanced tools for biomedical applications. Journal of Biotechnology 259, 148–159.
| Peptide nucleic acids: advanced tools for biomedical applications.Crossref | GoogleScholarGoogle Scholar | 28764969PubMed |
Hagedorn PH, Persson R, Funder ED, Albæk N, Diemer SL, Hansen DJ, Møller MR, Papargyri N, Christiansen H, Hansen BR, Hansen HF, Jensen MA, Koch T (2018) Locked nucleic acid: modality, diversity, and drug discovery. Drug Discovery Today 23, 101–114.
| Locked nucleic acid: modality, diversity, and drug discovery.Crossref | GoogleScholarGoogle Scholar | 28988994PubMed |
Heasman J (2002) Morpholino oligos: making sense of antisense? Developmental Biology 243, 209–214.
| Morpholino oligos: making sense of antisense?Crossref | GoogleScholarGoogle Scholar | 11884031PubMed |
Huang H, Wang Z, Cheng J, Zhao W, Li X, Wang H, Zhang Z, Sui X (2013) An efficient cucumber (Cucumis sativus L.) protoplast isolation and transient expression system. Scientia Horticulturae 150, 206–212.
| An efficient cucumber (Cucumis sativus L.) protoplast isolation and transient expression system.Crossref | GoogleScholarGoogle Scholar |
Janicka-Russak M, Kabała K, Wdowikowska A, Kłobus G (2012) Response of plasma membrane H+-ATPase to low temperaturę in cucumber roots. Journal of Plant Research 125, 291–300.
| Response of plasma membrane H+-ATPase to low temperaturę in cucumber roots.Crossref | GoogleScholarGoogle Scholar | 21638005PubMed |
Janicka-Russak M, Kabała K, Wdowikowska A, Kłobus G (2013) Modification of plasma membrane proton pumps in cucumber roots as an adaptation mechanism to salt stress. Journal of Plant Physiology 170, 915–922.
| Modification of plasma membrane proton pumps in cucumber roots as an adaptation mechanism to salt stress.Crossref | GoogleScholarGoogle Scholar | 23499455PubMed |
Jin Y, Fei M, Rosenquist S, Jin L, Gohil S, Sandström C, Olsson H, Persson C, Höglund A-S, Fransson G, Ruan Y, Åman P, Jansson C, Liu C, Andersson R, Sun C (2017) A dual-promoter gene orchestrates the sucrose-coordinated synthesis of starch and fructan in barley. Molecular Plant 10, 1556–1570.
| A dual-promoter gene orchestrates the sucrose-coordinated synthesis of starch and fructan in barley.Crossref | GoogleScholarGoogle Scholar | 29126994PubMed |
Juliano R, Alam MR, Dixit V, Kang H (2008) Mechanisms and strategies for effective delivery of antisense and siRNA oligonucleotides. Nucleic Acids Research 36, 4158–4171.
| Mechanisms and strategies for effective delivery of antisense and siRNA oligonucleotides.Crossref | GoogleScholarGoogle Scholar | 18558618PubMed |
Kang H, Fisher MH, Xu D, Miyamoto YJ, Marchand A, Van Aerschot A, Herdewijn P, Juliano RL (2004) Inhibition of MDR1 gene expression by chimeric HNA antisense oligonucleotides. Nucleic Acids Research 32, 4411–4419.
| Inhibition of MDR1 gene expression by chimeric HNA antisense oligonucleotides.Crossref | GoogleScholarGoogle Scholar | 15316104PubMed |
Khvorova A, Watts JK (2017) The chemical evolution of oligonucleotide therapies of clinical utility. Nature Biotechnology 35, 238–248.
| The chemical evolution of oligonucleotide therapies of clinical utility.Crossref | GoogleScholarGoogle Scholar | 28244990PubMed |
Koziołkiewicz M (1998) Antisense strategy--new trends. Postepy Biochemii 44, 125–135. [in Polish]
Kurreck J (2003) Antisense technologies. Improvement through novel chemical modifications. European Journal of Biochemistry 270, 1628–1644.
| Antisense technologies. Improvement through novel chemical modifications.Crossref | GoogleScholarGoogle Scholar | 12694176PubMed |
Lennox KA, Behlke MA (2011) Chemical modification and design of anti-miRNA oligonucleotides. Gene Therapy 18, 1111–1120.
| Chemical modification and design of anti-miRNA oligonucleotides.Crossref | GoogleScholarGoogle Scholar | 21753793PubMed |
Levin AA (1999) A review of issues in the pharmacokinetics and toxicology of phosphorothioate antisense oligonucleotides. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1489, 69–84.
| A review of issues in the pharmacokinetics and toxicology of phosphorothioate antisense oligonucleotides.Crossref | GoogleScholarGoogle Scholar |
Liang XH, Sun H, Shen W, Crooke ST (2015) Identification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages. Nucleic Acids Research 43, 2927–2945.
| Identification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages.Crossref | GoogleScholarGoogle Scholar | 25712094PubMed |
Liang XH, Sun H, Shen W, Wang S, Yao J, Migawa MT, Bui HH, Damle SS, Riney S, Graham MJ, Crooke RM, Crooke ST (2017) Antisense oligonucleotides targeting translation inhibitory elements in 5′ UTRs can selectively increase protein levels. Nucleic Acids Research 45, 9528–9546.
| Antisense oligonucleotides targeting translation inhibitory elements in 5′ UTRs can selectively increase protein levels.Crossref | GoogleScholarGoogle Scholar | 28934489PubMed |
Liao F, Wang L, Yang LB, Zhang L, Peng X, Sun MX (2013) Antisense oligodeoxynucleotide inhibition as an alternative and convenient method for gene function analysis in pollen tubes. PLoS ONE 8, e59112
| Antisense oligodeoxynucleotide inhibition as an alternative and convenient method for gene function analysis in pollen tubes.Crossref | GoogleScholarGoogle Scholar | 23527102PubMed |
Lu ZJ, Mathews DH (2008) Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. Nucleic Acids Research 36, 3738–3745.
| Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.Crossref | GoogleScholarGoogle Scholar | 18483081PubMed |
Manoharan M (1999) 2′-Carbohydrate modifications in antisense oligonucleotide therapy: importance of conformation, configuration and conjugation. Biochimica et Biophysica Acta (BBA) – Gene Structure and Expression 1489, 117–130.
| 2′-Carbohydrate modifications in antisense oligonucleotide therapy: importance of conformation, configuration and conjugation.Crossref | GoogleScholarGoogle Scholar |
Matveeva OV, Tsodikov AD, Giddings M, Freier SM, Wyatt JR, Spiridonov AN, Shabalina SA, Gesteland RF, Atkins JF (2000) Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity. Nucleic Acids Research 28, 2862–2865.
| Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity.Crossref | GoogleScholarGoogle Scholar | 10908347PubMed |
McQuisten KA, Peek AS (2007) Identification of sequence motifs significantly associated with antisense activity. BMC Bioinformatics 8, 184
| Identification of sequence motifs significantly associated with antisense activity.Crossref | GoogleScholarGoogle Scholar | 17555590PubMed |
Moutinho A, Camacho L, Haley A, et al. (2001) Antisense perturbation of protein function in living pollen tubes. Sexual Plant Reproduction 14, 101–104.
| Antisense perturbation of protein function in living pollen tubes.Crossref | GoogleScholarGoogle Scholar |
Moutinho A, Hussey PJ, Trewavas AJ, Malhó R (2001) cAMP acts as a second messenger in pollen tube growth and reorientation. Proceedings of the National Academy of Sciences of the United States of America 98, 10481–10486.
| cAMP acts as a second messenger in pollen tube growth and reorientation.Crossref | GoogleScholarGoogle Scholar | 11517303PubMed |
Pellestor F, Paulasova P (2004) The peptide nucleic acids (PNAs), powerful tools for molecular genetics and cytogenetics. European Journal of Human Genetics 12, 694–700.
| The peptide nucleic acids (PNAs), powerful tools for molecular genetics and cytogenetics.Crossref | GoogleScholarGoogle Scholar | 15213706PubMed |
Raal FJ, Santos RD, Blom DJ, Marais AD, Charng MJ, Cromwell WC, Lachmann RH, Gaudet D, Tan JL, Chasan-Taber S, Tribble DL, Flaim JD, Crooke ST (2010) Mipomersen, an apolipoprotein B synthesis inhibitor, for lowering of LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia: a randomised, double-blind, placebo-controlled trial. The Lancet 375, 998–1006.
| Mipomersen, an apolipoprotein B synthesis inhibitor, for lowering of LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia: a randomised, double-blind, placebo-controlled trial.Crossref | GoogleScholarGoogle Scholar |
Richter S, Müller LM, Stierhof Y-D, Mayer U, Takada N, Kost B, Vieten A, Geldner N, Koncz C, Jürgens G (2012) Polarized cell growth in Arabidopsis requires endosomal recycling mediated by GBF1-related ARF exchange factors. Nature Cell Biology 14, 80–86.
| Polarized cell growth in Arabidopsis requires endosomal recycling mediated by GBF1-related ARF exchange factors.Crossref | GoogleScholarGoogle Scholar |
Sohail M, Southern EM (2000) Selecting optimal antisense reagents. Advanced Drug Delivery Reviews 44, 23–34.
| Selecting optimal antisense reagents.Crossref | GoogleScholarGoogle Scholar | 11035195PubMed |
Sparkes IA, Runions J, Kearns A, Hawes C (2006) Rapid, transientexpression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants. Nature Protocols 1, 2019–2025.
| Rapid, transientexpression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants.Crossref | GoogleScholarGoogle Scholar | 17487191PubMed |
Sun C, Höglund A-S, Olsson H, Mangelsen E, Jansson C (2005) Antisense oligodeoxynucleotide inhibition as a potent strategy in plant biology: identification of SUSIBA2 as a transcriptional activator in plant sugar signalling. The Plant Journal 44, 128–138.
| Antisense oligodeoxynucleotide inhibition as a potent strategy in plant biology: identification of SUSIBA2 as a transcriptional activator in plant sugar signalling.Crossref | GoogleScholarGoogle Scholar | 16167901PubMed |
Sun C, Ridderstråle K, Höglund A-S, Larsson L-G, Jansson C (2007) Sweet delivery – sugar translocators as ports of entry for antisense oligodeoxynucleotides in plant cells. The Plant Journal 52, 1192–1198.
| Sweet delivery – sugar translocators as ports of entry for antisense oligodeoxynucleotides in plant cells.Crossref | GoogleScholarGoogle Scholar | 17922813PubMed |
Sun C, Ghebramedhin H, Höglund A-S, Jansson C (2008) Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology. Plant Signaling & Behavior 3, 328–330.
| Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology.Crossref | GoogleScholarGoogle Scholar |
Sundar IK, Sakthivel N (2008) Advances in selectable marker genes for plant transformation. Journal of Plant Physiology 165, 1698–1716.
| Advances in selectable marker genes for plant transformation.Crossref | GoogleScholarGoogle Scholar | 18789557PubMed |
Tolou H (1993) Administration of oligonucleotides to cultured cells by calcium phosphate precipitation method. Analytical Biochemistry 215, 156–158.
| Administration of oligonucleotides to cultured cells by calcium phosphate precipitation method.Crossref | GoogleScholarGoogle Scholar | 8297007PubMed |
Tsutsumi N, Kanayama K, Tano S (1992) Suppression of alpha-amylase gene expression by antisense oligodeoxynucleotide in barley cultured aleurone layers. The Japanese Journal of Genetics 67, 147–154.
| Suppression of alpha-amylase gene expression by antisense oligodeoxynucleotide in barley cultured aleurone layers.Crossref | GoogleScholarGoogle Scholar | 1524833PubMed |
Vickers TA, Crooke ST (2014) Antisense oligonucleotides capable of promoting specific target mRNA reduction via competing RNase H1-dependent and independent mechanisms. PLoS ONE 9, e108625
| Antisense oligonucleotides capable of promoting specific target mRNA reduction via competing RNase H1-dependent and independent mechanisms.Crossref | GoogleScholarGoogle Scholar | 25299183PubMed |
Wang S, Ku SS, Ye X, He C, Kwon SY, Choi PS (2015) Current status of genetic transformation technology developed in cucumber (Cucumis sativus L.). Journal of Integrative Agriculture 14, 469–482.
| Current status of genetic transformation technology developed in cucumber (Cucumis sativus L.).Crossref | GoogleScholarGoogle Scholar |
Wdowikowska A, Kłobus G (2016) The plasma membrane proton pump gene family in cucumber. Acta Physiologiae Plantarum 38, 135
| The plasma membrane proton pump gene family in cucumber.Crossref | GoogleScholarGoogle Scholar |
Wojtasik W, Kulma A, Boba A, Szopa J (2014) Oligonucleotide treatment causes flax β-glucanase up-regulation via changes in gene-body methylation. BMC Plant Biology 14, 261
| Oligonucleotide treatment causes flax β-glucanase up-regulation via changes in gene-body methylation.Crossref | GoogleScholarGoogle Scholar | 25287293PubMed |
Xie Z, Sundström JF, Jin Y, Liu C, Jansson C, Sun CA (2014) A selection strategy in plant transformation based on antisense oligodeoxynucleotide inhibition. The Plant Journal 77, 954–961.
| A selection strategy in plant transformation based on antisense oligodeoxynucleotide inhibition.Crossref | GoogleScholarGoogle Scholar | 24438514PubMed |
Yao Y, Wang C, Varshney RR, Wang DA (2009) Antisense makes sense in engineered regenerative medicine. Pharmaceutical Research 26, 263–275.
| Antisense makes sense in engineered regenerative medicine.Crossref | GoogleScholarGoogle Scholar | 19015958PubMed |
Yoo BH, Bochkareva E, Bochkarev A, Mou TC, Gray DM (2004) 2′-O-Methyl-modified phosphorothioate antisense oligonucleotides have reduced non-specific effects in vitro. Nucleic Acids Research 32, 2008–2016.
| 2′-O-Methyl-modified phosphorothioate antisense oligonucleotides have reduced non-specific effects in vitro.Crossref | GoogleScholarGoogle Scholar | 15064360PubMed |
Zamecnik PC, Stephenson ML (1978) Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proceedings of the National Academy of Sciences of the United States of America 75, 280–284.
| Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide.Crossref | GoogleScholarGoogle Scholar |
Zhang M, Wang Y, Chen X, et al. (2021) Plasma membrane H+-ATPase overexpression increases rice yield via simultaneous enhancement of nutrient uptake and photosynthesis. Nature Communications 12, 735
| Plasma membrane H+-ATPase overexpression increases rice yield via simultaneous enhancement of nutrient uptake and photosynthesis.Crossref | GoogleScholarGoogle Scholar | 33531490PubMed |
Zhao M, Zhang N, Gao T, Jin J, Jing T, Wang J, Wu Y, Wan X, Schwab W, Song C (2020) Sesquiterpene glucosylation mediated by glucosyltransferase UGT91Q2 is involved in the modulation of cold stress tolerance in tea plants. New Phytologist 226, 362–372.
| Sesquiterpene glucosylation mediated by glucosyltransferase UGT91Q2 is involved in the modulation of cold stress tolerance in tea plants.Crossref | GoogleScholarGoogle Scholar |
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31, 3406–3415.
| Mfold web server for nucleic acid folding and hybridization prediction.Crossref | GoogleScholarGoogle Scholar | 12824337PubMed |
Zuker M (2010) Mfold©: RNA modeling program. GERF Bulletin of Biosciences 1, 1–6.
