Same modification, different location: the mythical role of N6-adenine methylation in plant genomes

Pijeira‐Fernández, Gema; Moreno-Cálix, Delia M.; De‐la‐Peña, Clelia

doi:10.1007/s00425-022-03926-y

Cited by 5 publications

(4 citation statements)

References 94 publications

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“…It has been shown that m6A had a regulatory function on selective shearing of pre-mRNA and processing of mRNA at the post-transcriptional level and then affected mRNA stability, translation, secondary structure and transport. Currently, most of the m6A-related studies were conducted in animals, especially in human [ 6 , 7 ]. With the advancement of detection technology, the related studies have gradually been performed in plants, mainly in model species, such as Arabidopsis and rice [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii

Lin

Shi

Zhang

et al. 2023

Plants

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N6-methyladenosine modifications (m6A) is one of the most abundant and prevalent post-transcriptional RNA modifications in plants, playing the crucial role in plant growth and development and stress adaptation. However, the m6A regulatory machinery in Aegilops_tauschii, the D genome progenitor of common wheat, is not well understood at present. Here, we systematically identified the m6A-related genes in Aegilops with a genome-wide search approach. In total, 25 putative m6A genes composed of 5 writers, 13 readers and 7 erasers were obtained. A phylogenetic analysis clearly grouped them into three subfamilies with the same subfamily showing similar gene structures and conserved domains. These m6A genes were found to contain a large number of cis-acting elements associating with plant hormones, regulation of growth and development as well as stress response, suggesting their widespread regulation function. Furthermore, the expression profiling of them was investigated using RNA-seq data to obtain stress-responsive candidates, of which 5 were further validated with a qPCR analysis. Finally, the genetic variation of m6A-related genes was investigated between Aegilops and D subgenome of wheat based on re-sequencing data, and an obvious genetic bottleneck occurred on them during the wheat domestication process. The promising haplotype association with domestication and agronomic traits was also detected. This study provided some insights on the genomic organization and evolutionary features of m6A-related genes in Aegilops, which will facilitate the further functional study and also contribute to broaden the genetic basis for genetic improvement in wheat and other crops.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii

Lin

Shi

Zhang

et al. 2023

Plants

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“…DNA can be also methylated at N6 position in adenine (N6mA) and is predominant in fungi, ciliates and green algae. Intriguingly, it was also detected in several plant species including Arabidopsis and important crops like, rice, wheat and soybean ( Jiménez-Ramírez et al., 2022 ; Varma et al., 2022 ). However, reports on N6mA’s regulatory roles in plants are still scarce.…”

Section: Introductionmentioning

confidence: 99%

The role of epigenetic and epitranscriptomic modifications in plants exposed to non-essential metals

Chmielowska-Bąk,

Searle,

Wakai

et al. 2023

Front. Plant Sci.

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Contamination of the soil with non-essential metals and metalloids is a serious problem in many regions of the world. These non-essential metals and metalloids are toxic to all organisms impacting crop yields and human health. Crop plants exposed to high concentrations of these metals leads to perturbed mineral homeostasis, decreased photosynthesis efficiency, inhibited cell division, oxidative stress, genotoxic effects and subsequently hampered growth. Plants can activate epigenetic and epitranscriptomic mechanisms to maintain cellular and organism homeostasis. Epigenetic modifications include changes in the patterns of cytosine and adenine DNA base modifications, changes in cellular non-coding RNAs, and remodeling histone variants and covalent histone tail modifications. Some of these epigenetic changes have been shown to be long-lasting and may therefore contribute to stress memory and modulated stress tolerance in the progeny. In the emerging field of epitranscriptomics, defined as chemical, covalent modifications of ribonucleotides in cellular transcripts, epitranscriptomic modifications are postulated as more rapid modulators of gene expression. Although significant progress has been made in understanding the plant’s epigenetic changes in response to biotic and abiotic stresses, a comprehensive review of the plant’s epigenetic responses to metals is lacking. While the role of epitranscriptomics during plant developmental processes and stress responses are emerging, epitranscriptomic modifications in response to metals has not been reviewed. This article describes the impact of non-essential metals and metalloids (Cd, Pb, Hg, Al and As) on global and site-specific DNA methylation, histone tail modifications and epitranscriptomic modifications in plants.

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“…Only recently, it became evident that DNA adenine methylation plays an important role in epigenetic regulation of vital processes in plants [ 21 , 22 , 23 ]. In particular, the evidence has been obtained that DNA methylation of adenine is essential in developmental processes and in stress response of rice [ 24 , 25 ], in the transition from vegetative to reproductive growth in Arabidopsis [ 20 ], and in fruit development of sea buckthorn [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

“…In particular, the evidence has been obtained that DNA methylation of adenine is essential in developmental processes and in stress response of rice [ 24 , 25 ], in the transition from vegetative to reproductive growth in Arabidopsis [ 20 ], and in fruit development of sea buckthorn [ 26 ]. It is becoming evident that 6m A is complementary to 5m C as a gene expression epigenomic mark in eukaryotes, carrying essential biophysical properties that affect the stability of nucleic acids and their binding affinity with other molecules, thus providing the changes in gene expression, DNA replication, and repair mechanisms [ 22 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

Light Dependent Changes in Adenylate Methylation of the Promoter of the Mitochondrial Citrate Synthase Gene in Maize (Zea mays L.) Leaves

Епринцев

Федорин

Igamberdiev

2022

IJMS

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Limited methyl-specific restriction of genomic DNA by endonuclease MAL1 revealed the changes in its methyl status caused by adenine modification in maize (Zea mays L.) leaves under different light conditions (dark, light, irradiation by red and far-red light). Incubation in the light and irradiation by red light exhibited an activating effect on DNA adenine methylase activity, which was reflected in an increase in the number of methylated adenines in GATC sites. Far-red light and darkness exhibited an opposite effect. The use of nitrite conversion of DNA followed by methyladenine-dependent restriction by MboI nuclease revealed a phytochrome B-dependent mechanism of regulation of the methyl status of adenine in the GATC sites in the promoter of the gene encoding the mitochondrial isoform of citrate synthase. Irradiation of plants with red light caused changes in the adenine methyl status of the analyzed amplicon, as evidenced by the presence of restriction products of 290, 254, and 121 nucleotides. Adenine methylation occurred at all three GATC sites in the analyzed DNA sequence. It is concluded that adenylate methylation is controlled by phytochrome B via the transcription factor PIF4 and represents an important mechanism for the tricarboxylic acid cycle regulation by light.

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Same modification, different location: the mythical role of N6-adenine methylation in plant genomes

Cited by 5 publications

References 94 publications

Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii

Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii

The role of epigenetic and epitranscriptomic modifications in plants exposed to non-essential metals

Light Dependent Changes in Adenylate Methylation of the Promoter of the Mitochondrial Citrate Synthase Gene in Maize (Zea mays L.) Leaves

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