Dynamics of DNA Methylation and Its Functions in Plant Growth and Development

Abstract

Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.

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“…Така мінливість, як припускається, дозволяє рослинам адаптуватися до мінливих умов навколишнього середовища в часі, занадто короткому для виникнення адаптивних мутацій (Lachmann, Jablonka, 1996;Brautigam et al, 2013;Meyer, 2015;Ashapkin et al, 2016;Lebedeva et al, 2017). Метилування цитозину ДНК розглядається як основний молекулярний механізм, що забезпечує важливу геномну інформацію та сприяє розумінню молекулярних основ фенотипічних варіацій на основі епігенетичних модифікацій в еукаріотичних організмах, хоча рівні та закономірності метилування ДНК істотно відмінні у різних організмів (Saze et al, 2003;Peng, Zhang, 2009;Dowen et al, 2012;Herman, Sultan, 2016;Zhang et al, 2018;Kumar, Mohapatra, 2021).…”

DNA Methylation of ABC Transporters Differs in Native and Non-native Populations of Conyza canadensis L.

“…DNA methylation, one of the most common epigenetic modifications, contributes to the overall growth, development, and tolerance to both biotic and abiotic factors (Alonso et al, 2018;Agarwal et al, 2020;Eriksson et al, 2020;Gallego-Bartolom, 2020;Liu and He, 2020;Kumar and Mohapatra, 2021). DNA methylation and other epigenetic modifications are now known to adjust phenotypes instantaneously and/or generate new phenotypes in a reversibly heritable manner (Flatscher et al, 2012;Miryeganeh and Saze, 2019).…”

Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

“…It is now evident that the information and function of a genome are modulated under varying environmental conditions not only by the epigenetic modifications in the linear DNA sequence but also by altering the 3D chromatin organization within the nucleus ( Dogan and Liu, 2018 ; Grob, 2020 ). Gene activities are controlled/regulated by alterations in chromatin architecture via DNA methylation ( Kumar et al, 2018 ; Kumar and Mohapatra, 2021 ), histone modifications ( Rowley et al, 2017 ; Park et al, 2018 ), and chromatin remodelers ( Peterson and Workman, 2000 ; Bhadouriya et al, 2021 ). Different chromatin remodelers such as CHD, INO80, ISWI, and Switch/Sucrose non-fermenting (SWI/SNF) have been reported to act upon chromatin under diverse environmental stresses to convert transcriptionally inactive chromatin to the transcriptionally active state.…”

“…Tight coiling of chromatin (a default state) restricts transcriptional expression of the gene, which gets expressed when the nearby chromatin is loosened (remodeled) ( Bannister and Kouzarides, 2011 ). The accumulating datasets on epigenomics ( Kumar and Mohapatra, 2021 ) and the evident roles of genome architecture on the regulation of gene expression ( Zhang and Wang, 2021 ) indicate that 3D genomics would be an important player in deciphering the key regulators. Developmental and environmental stimuli affect epigenetic landscape and chromatin architecture, which are dynamic and modulate gene expression to cope with stress ( Bhadouriya et al, 2021 ).…”