Same Modification, Different Location: the Mythical Role of N-adenine Methylation in Plant Genomes

Overview

Journal Planta

Specialty Biology

Date 2022 Jun 13

PMID 35696004

Authors

Irma A Jimenez-Ramirez

Gema Pijeira-Fernandez

Delia M Moreno-Calix

Clelia De-la-Pena

Affiliations

Soon will be listed here.

Abstract

The present review summarizes recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics, discusses its importance in plant genomes, and highlights its chemical nature and functions. Adenine methylation is an epigenetic modification present in DNA (6mA) and RNA (m6A) that has a regulatory function in many cellular processes. This modification occurs through a reversible reaction that covalently binds a methyl group, usually at the N position of the purine ring. This modification carries biophysical properties that affect the stability of nucleic acids as well as their binding affinity with other molecules. DNA 6mA has been related to genome stability, gene expression, DNA replication, and repair mechanisms. Recent advances have shown that 6mA in plant genomes is related to development and stress response. In this review, we present recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics. We discuss the key elements of this modification, focusing mainly on its importance in plant genomes. Furthermore, we highlight its chemical nature and the regulatory effects that it exerts on gene expression and plant development. Finally, we emphasize the functions of 6mA in photosynthesis, stress, and flowering.

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References

Achwal C, Iyer C, Chandra H . Immunochemical evidence for the presence of 5mC, 6mA and 7mG in human, Drosophila and mealybug DNA. FEBS Lett. 1983; 158(2):353-8. DOI: 10.1016/0014-5793(83)80612-7. View

Beh L, Debelouchina G, Clay D, Thompson R, Lindblad K, Hutton E . Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization. Cell. 2019; 177(7):1781-1796.e25. PMC: 6570567. DOI: 10.1016/j.cell.2019.04.028. View

Boulias K, Greer E . The adenine methylation debate. Science. 2022; 375(6580):494-495. PMC: 9383032. DOI: 10.1126/science.abn6514. View

Boulias K, Greer E . Means, mechanisms and consequences of adenine methylation in DNA. Nat Rev Genet. 2022; 23(7):411-428. PMC: 9354840. DOI: 10.1038/s41576-022-00456-x. View

Buchmuller B, Jung A, Munoz-Lopez A, Summerer D . Programmable tools for targeted analysis of epigenetic DNA modifications. Curr Opin Chem Biol. 2021; 63:1-10. DOI: 10.1016/j.cbpa.2021.01.002. View

Chachar S, Liu J, Zhang P, Riaz A, Guan C, Liu S . Harnessing Current Knowledge of DNA N6-Methyladenosine From Model Plants for Non-model Crops. Front Genet. 2021; 12:668317. PMC: 8118384. DOI: 10.3389/fgene.2021.668317. View

Collier J, McAdams H, Shapiro L . A DNA methylation ratchet governs progression through a bacterial cell cycle. Proc Natl Acad Sci U S A. 2007; 104(43):17111-6. PMC: 2040471. DOI: 10.1073/pnas.0708112104. View

Dhar M, Pethe V, Gupta V, Ranjekar P . Predominance and tissue specificity of adenine methylation in rice. Theor Appl Genet. 2013; 80(3):402-8. DOI: 10.1007/BF00210080. View

Douvlataniotis K, Bensberg M, Lentini A, Gylemo B, Nestor C . No evidence for DNA -methyladenine in mammals. Sci Adv. 2020; 6(12):eaay3335. PMC: 7080441. DOI: 10.1126/sciadv.aay3335. View

10.

DUNN D, Smith J . Occurrence of a new base in the deoxyribonucleic acid of a strain of Bacterium coli. Nature. 1955; 175(4451):336-7. DOI: 10.1038/175336a0. View

11.

Engel J, von Hippel P . Effects of methylation on the stability of nucleic acid conformations: studies at the monomer level. Biochemistry. 1974; 13(20):4143-58. DOI: 10.1021/bi00717a013. View

12.

Fedeles B, Singh V, Delaney J, Li D, Essigmann J . The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond. J Biol Chem. 2015; 290(34):20734-20742. PMC: 4543635. DOI: 10.1074/jbc.R115.656462. View

13.

Fedoreyeva L, Vanyushin B . N(6)-Adenine DNA-methyltransferase in wheat seedlings. FEBS Lett. 2002; 514(2-3):305-8. DOI: 10.1016/s0014-5793(02)02384-0. View

14.

Fu Y, Luo G, Chen K, Deng X, Yu M, Han D . N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell. 2015; 161(4):879-892. PMC: 4427561. DOI: 10.1016/j.cell.2015.04.010. View

15.

Graham M, Larkin P . Adenine methylation at dam sites increases transient gene expression in plant cells. Transgenic Res. 1995; 4(5):324-31. DOI: 10.1007/BF01972529. View

16.

Gray M . Lynn Margulis and the endosymbiont hypothesis: 50 years later. Mol Biol Cell. 2017; 28(10):1285-1287. PMC: 5426843. DOI: 10.1091/mbc.E16-07-0509. View

17.

Greer E, Blanco M, Gu L, Sendinc E, Liu J, Aristizabal-Corrales D . DNA Methylation on N6-Adenine in C. elegans. Cell. 2015; 161(4):868-78. PMC: 4427530. DOI: 10.1016/j.cell.2015.04.005. View

18.

Hao Z, Wu T, Cui X, Zhu P, Tan C, Dou X . N-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA. Mol Cell. 2020; 78(3):382-395.e8. PMC: 7214128. DOI: 10.1016/j.molcel.2020.02.018. View

19.

Heyn H, Esteller M . An Adenine Code for DNA: A Second Life for N6-Methyladenine. Cell. 2015; 161(4):710-3. DOI: 10.1016/j.cell.2015.04.021. View

20.

Hu J, Cai J, Park S, Lee K, Li Y, Chen Y . N -Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. Plant J. 2021; 106(6):1759-1775. DOI: 10.1111/tpj.15270. View