RNA methylation in plants: An overview

Abstract

RNA methylation is an important post-transcriptional modification that influences gene regulation. Over 200 different types of RNA modifications have been identified in plants. In animals, the mystery of RNA methylation has been revealed, and its biological role and applications have become increasingly clear. However, RNA methylation in plants is still poorly understood. Recently, plant science research on RNA methylation has advanced rapidly, and it has become clear that RNA methylation plays a critical role in plant development. This review summarizes current knowledge on RNA methylation in plant development. Plant writers, erasers, and readers are highlighted, as well as the occurrence, methods, and software development in RNA methylation is summarized. The most common and abundant RNA methylation in plants is N6-methyladenosine (m6A). In Arabidopsis, mutations in writers, erasers, and RNA methylation readers have affected the plant’s phenotype. It has also been demonstrated that methylated TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1-messenger RNA moves from shoot to root while unmethylated TCTP1-mRNA does not. Methylated RNA immunoprecipitation, in conjunction with next-generation sequencing, has been a watershed moment in plant RNA methylation research. This method has been used successfully in rice, Arabidopsis, Brassica, and maize to study transcriptome-wide RNA methylation. Various software or tools have been used to detect methylated RNAs at the whole transcriptome level; the majority are model-based analysis tools (for example, MACS2). Finally, the limitations and future prospects of methylation of RNA research have been documented.

Emerging Roles of RNA Methylation in Development

“…RNA m 6 A modification was also found to be markedly increased throughout brain development . For plant growth, PtrMTA is responsible for the formation of m 6 A in poplar and regulate the root development and the tolerance of drought stress. Hormone responses related modified RNAs express more actively than the non-modified ones with increased m 6 A levels during tomato fruit expansion.…”

RNA N6-adenine methylation dynamics impactHyaloperonospora arabidopsidisresistance inArabidopsis

“…Epitranscriptome comprises over 170 RNA modifications, with N6-adenine methylation (m6A) being the most extensively studied and abundant in eukaryotes, particularly in mRNA (Shinde et al, 2023). In the model plant Arabidopsis thaliana , m6A is deposited by a complex of methyltransferases mRNA adenosine methylase A (MTA, homolog of mammalian METTL3) and methyltransferase B (MTB, homolog of mammalian METTL14), along with cofactors VIRILIZER (VIR, homolog of mammalian VIRMA), E3 ubiquitin ligase AtHAKAI (homolog of mammalian HAKAI) and FKBP12 INTERACTING PROTEIN 37 (FIP37, homolog of mammalian WTAP) (Růžička et al, 2017; Shen, 2023).…”

“…In the model plant Arabidopsis thaliana , m6A is deposited by a complex of methyltransferases mRNA adenosine methylase A (MTA, homolog of mammalian METTL3) and methyltransferase B (MTB, homolog of mammalian METTL14), along with cofactors VIRILIZER (VIR, homolog of mammalian VIRMA), E3 ubiquitin ligase AtHAKAI (homolog of mammalian HAKAI) and FKBP12 INTERACTING PROTEIN 37 (FIP37, homolog of mammalian WTAP) (Růžička et al, 2017; Shen, 2023). In mRNA, m6A is deposited at the RRACH (R = A/G, H = A/U/C) consensus motif, and is mostly prevalent near start/stop codons and at 3’ untranslated regions (3′-UTRs) of mature mRNAs (Shinde et al ., 2023). Several studies in different eukaryotic systems have shown that m6A modulates mRNAs fate in cells, by affecting mRNA stability and half-life, alternative splicing, mRNA translation, nucleo-cytoplasmic export rates, and m6A-mediated phase separation (Zaccara et al, 2019).…”

“…Several studies in different eukaryotic systems have shown that m6A modulates mRNAs fate in cells, by affecting mRNA stability and half-life, alternative splicing, mRNA translation, nucleo-cytoplasmic export rates, and m6A-mediated phase separation (Zaccara et al, 2019). Removal of m6A is mediated by α-ketoglutarate-dependent dioxygenase homolog (ALKBH) proteins, such as ALKBH9B and ALKBH10B (Shinde et al ., 2023) in Arabidopsis (Mielecki et al, 2012). Recent studies reveal that abiotic environmental cues such as salt, cold or heat stresses dynamically modulate N6-adenine (de)methylation (Hu et al, 2021; Wang et al, 2022a).…”

Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet

“…This study also reported photosynthesis, plant hormone signal transduction, and mitogen-activated kinase signaling as a drought-responsive pathway [ 10 ]. The function of several abiotic-stress-responsive genes and small RNAs has been studied in several plants [ 11 ] and pearl millet [ 12 , 13 , 14 , 15 , 16 ]. However, knowledge of molecular mechanisms regulating physiological responses is equally critical and important for ensuring the quality and yield of plants.…”