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Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses

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Plant Abiotic Stress Signaling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2642))

Abstract

Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as “non-B DNA” structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.

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Acknowledgments

This work was supported by the Czech Science Foundation (GAČR 21-18532S to Adriana Volná, Jakub Nezval, Radomír Pech, and Vladimír Špunda) and the University of Ostrava (SGS11/PřF/2022 to Adriana Volná, Radomír Pech, and Jakub Nezval; SGS10/PřF/2022 to Petr Pečinka). Jiří Červeň, Petr Pečinka and Martin Bartas were supported by the National Agency for Agricultural Research (NAZV) of the Czech Republic grant no. QK1810391 “Utilization of genomic and transcriptomic approaches to create genetic resources and breeding materials of poppy with specific traits.” Participation of Radomír Pech was supported by the Moravian-Silesian Region (RRC/10/2021). Vladimír Špunda was supported by the Ministry of Education, Youth and Sports of the Czech Republic, project “SustES—Adaptation strategies for sustainable ecosystem services and food security under adverse environmental conditions” (CZ.02.1.01/0.0/0.0/16_019/0000797). Figures were created with BioRender.com.

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  1. Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic

    Adriana Volná, Jakub Nezval, Radomír Pech & Vladimír Špunda

  2. Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic

    Martin Bartas, Petr Pečinka & Jiří Červeň

  3. Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic

    Vladimír Špunda

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  1. UMR 6553 ECOBIO (Ecosystems-Biodiversity-Evolution), Centre National de la Recherche Scientifique (CNRS), University of Rennes, Rennes, France

    Ivan Couée

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Volná, A. et al. (2023). Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. In: Couée, I. (eds) Plant Abiotic Stress Signaling. Methods in Molecular Biology, vol 2642. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3044-0_18

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