FIONA1-mediated mRNA m6 A methylation regulates the response of Arabidopsis to salt stress

Genetic and Epigenetic Views of the Adaptive Evolution of Oaks (Quercus L.)

The long-lived angiosperm Quercus L. (Oaks) have emerged as promising model organisms for investigating adaptive divergence and ecological environmental interactions due to their longevity and large genetic diversity as well as recurrent gene flow among species with diverse natural habitats. Until recently, numerous genomic studies by new high-throughput sequencing platforms have provided access to link genes with ecological and physiological traits. However, the genetic and epigenetic mechanisms underlying the adaptive evolution of oak trees are still poorly understood. In this review, we summarise the current progress of reported oak genomes and inheritance systems, analysing the epigenetics and genetic structure of oaks. We review evidence regarding the genetic mechanism linking introgressive hybridisation and reproductive isolation for a better understanding of adaptive divergence and defining speciation in oaks. Furthermore, we also discuss the interaction and evolution between oaks, other organisms and the environment to explore the adaptive strategies and coevolutionary mechanisms among them. Through the impact of this article, hopefully, a distinctive avenue could be established to further study the inheritance, ecology and multidimensional evolution of oaks.

A review of m6A modification in plant development and potential quality improvement

N6-methyladenosine (m6A) represents the most prevalent internal modification observed in eukaryotic mRNAs. As a pivotal regulator of gene expression, m6A exerts influence over a number of processes, including splicing, transport, translation, degradation, and the stability of mRNAs. It thus plays a crucial role in plant development and resistance to biotic and abiotic stressors. The writers, erasers, and readers of m6A, which deposit, eliminate and decode this modification, are also of critical importance and have been identified and characterized in multiple plant species. The advent of next-generation sequencing (NGS) and m6A detection technologies has precipitated a surge in research on m6A in recent years. Extensive research has elucidated the specific roles of m6A in plants and its underlying molecular mechanisms, indicating significant potential for crop improvement. This review presents a comprehensive overview of recent studies on m6A and its regulatory proteins in plant development and stress tolerance. It highlights the potential applications of this modification and its writers, erasers, and readers for plant improvement, with a particular focus on leaf development, floral transition, trichome morphogenesis, fruit ripening, and resilience to pests, diseases and abiotic stresses.

MdDSK2a-Like-MdMTA Module Functions in Apple Cold Response via Regulating ROS Detoxification and Cell Wall Deposition

N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic cells. Although the importance of its roles in mRNA metabolism, plant development, and stress responses has been well documented, regulation of its machinery is largely unknown in plants. Here, it is reported that MdMTA positively regulates cold tolerance. Combining MeRIP-seq and RNA-seq, it is found that MdMTA regulates the m6A and expression levels of cold-responsive genes under cold stress, including those involved in reactive oxygen species (ROS) detoxification and cell wall deposition. Further analysis reveals that MdMTA promotes ROS scavenging and the deposition of cellulose and hemicellulose by regulating the mRNA stability of the relevant genes under cold conditions. MdDSK2a-like, a ubiquitin receptor protein, mediates MdMTA degradation by the 26S ubiquitin-dependent proteasome and autophagy pathways. MdDSK2a-like negatively regulates cold tolerance by reducing the m6A levels of MdMTA target genes. Consistently, MdDSK2a-like inhibits ROS scavenging and the deposition of cellulose and hemicellulose under cold conditions. Genetic dissection shows that MdDSK2a-like acts upstream of MdMTA in cold response. The results not only reveal the degradation of MdMTA, but also illustrate the molecular mechanism of the MdDSK2a-like-MdMTA module in m6A modification and cold response.

The RNA m6A Methyltransferase PheMTA1 and PheMTA2 of Moso Bamboo Regulate Root Development and Resistance to Salt Stress in Plant

As the most prevalent RNA modification in eukaryotes, N6-methyladenosine (m6A) plays a crucial role in regulating various biological processes in plants, including embryonic development and flowering. However, the function of m6A RNA methyltransferase in moso bamboo remains poorly understood. In this study, we identified two m6A methyltransferases in moso bamboo, PheMTA1 and PheMTA2. Overexpression of PheMTA1 and PheMTA2 significantly promoted root development and enhanced salt tolerance in rice. Using the HyperTRIBE method, we fused PheMTA1 and PheMTA2 with ADARcdE488Q and introduced them into rice. RNA sequencing (RNA-seq) of the overexpressing rice identified the target RNAs bound by PheMTA1 and PheMTA2. PheMTA1 and PheMTA2 bind to OsATM3 and OsSF3B1, which were involved in the development of root and salt resistance. Finally, we revealed the effects of transcription or alternative splicing on resistance-related genes like OsRS33, OsPRR73, OsAPX2 and OsHAP2E, which are associated with the observed phenotype. In conclusion, our study demonstrates that the m6A methyltransferases PheMTA1 and PheMTA2 from moso bamboo are involved in root development and enhance plant resistance to salt stress.

RNA modifications in plant adaptation to abiotic stresses

Epitranscriptomic chemical modifications of RNAs have emerged as potent regulatory mechanisms in the process of plant stress adaptation. Currently, over 170 distinct chemical modifications have been identified in mRNAs, tRNAs, rRNAs, microRNAs (miRNAs), and long noncoding RNAs (lncRNAs). Genetic and molecular studies have identified the genes responsible for addition and removal of chemical modifications from RNA molecules, which are known as "writers" and "erasers," respectively. N6-methyladenosine (m6A) is the most prevalent chemical modification identified in eukaryotic mRNAs. Recent studies have identified m6A writers and erasers across different plant species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), cotton (Gossypium hirsutum), and tomato (Solanum lycopersicum). Accumulating discoveries have improved our understanding of the functions of RNA modifications in plant stress responses. This review highlights the latest research on RNA modification, emphasizing the biological and cellular roles of diverse chemical modifications of mRNAs, tRNAs, rRNAs, miRNAs, and lncRNAs in plant responses to environmental and hormonal signals. We also propose and discuss critical questions and future challenges for enhancing our understanding of the cellular and mechanistic roles of RNA modifications in plant stress responses. Integrating molecular insights into the regulatory roles of RNA modifications in stress responses with novel genome- and RNA-editing technologies will facilitate the breeding of stress-tolerant crops through precise engineering of RNA modifications.

Epigenetic control of plant abiotic stress responses

On top of genetic information, organisms have evolved complex and sophisticated epigenetic regulation to adjust gene expression in response to developmental and environmental signals. Key epigenetic mechanisms include DNA methylation, histone modifications and variants, chromatin remodeling, and chemical modifications of RNAs. Epigenetic control of environmental responses is particularly important for plants, which are sessile and unable to move away from adverse environments. Besides enabling plants to rapidly respond to environmental stresses, some stress-induced epigenetic changes can be maintained, providing plants with a pre-adapted state to recurring stresses. Understanding these epigenetic mechanisms offers valuable insights for developing crop varieties with enhanced stress tolerance. Here, we focus on abiotic stresses and summarize recent progress in characterizing stress-induced epigenetic changes and their regulatory mechanisms and roles in plant abiotic stress resistance.

mRNA ADENOSINE METHYLASE promotes drought tolerance through N6-methyladenosine-dependent and independent impacts on mRNA regulation in Arabidopsis

Among many mRNA modifications, adenine methylation at the N6 position (N6-methyladenosine, m6A) is known to affect mRNA biology extensively. The influence of m6A has yet to be assessed under drought, one of the most impactful abiotic stresses. We show that Arabidopsis thaliana (L.) Heynh. (Arabidopsis) plants lacking mRNA ADENOSINE METHYLASE (MTA) are drought-sensitive. Subsequently, we comprehensively assess the impacts of MTA-dependent m6A changes during drought on mRNA abundance, stability, and translation in Arabidopsis. During drought, there is a global trend toward hypermethylation of many protein-coding transcripts that does not occur in mta. We also observe complex regulation of m6A at a transcript-specific level, possibly reflecting compensation by other m6A components. Importantly, a subset of transcripts that are hypermethylated in an MTA-dependent manner exhibited reduced turnover and translation in mta, compared with wild-type (WT) plants, during drought. Additionally, MTA impacts transcript stability and translation independently of m6A. We also correlate drought-associated deposition of m6A with increased translation of modulators of drought response, such as RD29A, COR47, COR413, ALDH2B, ERD7, and ABF4 in WT, which is impaired in mta. m6A is dynamic during drought and, alongside MTA, promotes tolerance by regulating drought-responsive changes in transcript turnover and translation.

ECT8, an mRNA m6A reader, enhances salt stress tolerance by modulating mRNA stability in Arabidopsis

N6-methyladenosine (m6A), the most prevalent modification found in eukaryotic mRNAs, is recognized and interpreted by m6A-binding proteins called m6A readers. The EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT) proteins have increasingly been identified as m6A readers in plants. A recent study has demonstrated that the loss-of-function ect8 mutant is sensitive to salt stress by enhancing the stability of negative salt stress regulators in Arabidopsis (Arabidopsis thaliana). In this study, we generated and analyzed the ECT8-overexpressing transgenic Arabidopsis plants to further explore the function of ECT8 in salt stress response. The electrophoretic mobility shift assay in vitro showed that ECT8 binds to the m6A-modified synthetic RNAs, preferring UGUm6AA and UACm6AGA motifs over the GGm6ACU motif. Contrary to the ect8 mutant exhibiting salt hypersensitivity by enhancing the stability of salt stress negative regulators, the ECT8-overexpressing transgenic Arabidopsis plants displayed salt tolerance by increasing the stability and expression levels of salt stress positive regulators. Moreover, RNA-immunoprecipitation assay demonstrated that ECT8 binds to the m6A-modified salt stress-responsive mRNAs in planta. Collectively, our current and previous findings highlight that ECT8-mediated stabilization and destabilization of the genes encoding salt stress positive or negative regulators, respectively, contribute to the salt stress tolerance of Arabidopsis.

Reading m6A marks in mRNA: A potent mechanism of gene regulation in plants

Modifications to RNA have recently been recognized as a pivotal regulator of gene expression in living organisms. More than 170 chemical modifications have been identified in RNAs, with N6-methyladenosine (m6A) being the most abundant modification in eukaryotic mRNAs. The addition and removal of m6A marks are catalyzed by methyltransferases (referred to as "writers") and demethylases (referred to as "erasers"), respectively. In addition, the m6A marks in mRNAs are recognized and interpreted by m6A-binding proteins (referred to as "readers"), which regulate the fate of mRNAs, including stability, splicing, transport, and translation. Therefore, exploring the mechanism underlying the m6A reader-mediated modulation of RNA metabolism is essential for a much deeper understanding of the epigenetic role of RNA modification in plants. Recent discoveries have improved our understanding of the functions of m6A readers in plant growth and development, stress response, and disease resistance. This review highlights the latest developments in m6A reader research, emphasizing the diverse RNA-binding domains crucial for m6A reader function and the biological and cellular roles of m6A readers in the plant response to developmental and environmental signals. Moreover, we propose and discuss the potential future research directions and challenges in identifying novel m6A readers and elucidating the cellular and mechanistic role of m6A readers in plants.

Crosstalk between RNA m6A modification and epigenetic factors in plant gene regulation

N6-methyladenosine (m6A) is the most abundant modification observed in eukaryotic mRNAs. Advances in transcriptome-wide m6A mapping and sequencing technologies have enabled the identification of several conserved motifs in plants, including the RRACH (R = A/G and H = A/C/U) and UGUAW (W = U or A) motifs. However, the mechanisms underlying deposition of m6A marks at specific positions in the conserved motifs of individual transcripts remain to be clarified. Evidence from plant and animal studies suggests that m6A writer or eraser components are recruited to specific genomic loci through interactions with particular transcription factors, 5-methylcytosine DNA methylation marks, and histone marks. In addition, recent studies in animal cells have shown that microRNAs play a role in depositing m6A marks at specific sites in transcripts through a base-pairing mechanism. m6A also affects the biogenesis and function of chromatin-associated regulatory RNAs and long noncoding RNAs. Although we have less of an understanding of the link between m6A modification and epigenetic factors in plants than in animals, recent progress in identifying the proteins that interact with m6A writer or eraser components has provided insights into the crosstalk between m6A modification and epigenetic factors, which plays a crucial role in transcript-specific methylation and regulation of m6A in plants.

Genome-Wide Identification and Expression Analysis of the ALKB Homolog Gene Family in Potato (Solanum tuberosum L.)

N6-methyladenosine (m6A) is an abundant and pervasive post-transcriptional modification in eukaryotic mRNAs. AlkB homolog (ALKBH) proteins play crucial roles in RNA metabolism and translation, participating in m6A methylation modification to regulate plant development. However, no comprehensive investigations have been conducted on ALKBH in potato. Here, 11 StALKBH family genes were identified in potato and renamed according to BLASTP and phylogenetic analyses following the Arabidopsis genome. The characteristics, sequence structures, motif compositions, phylogenetics, chromosomal locations, synteny, and promoter cis-acting element predictions were analyzed, revealing distinct evolutionary relationships between potato and other species (tomato and Arabidopsis). Homologous proteins were classified into seven groups depending on similar conserved domains, which implies that they possess a potentially comparable function. Moreover, the StALKBHs were ubiquitous, and their expression was examined in the various tissues of a whole potato, in which the StALKBH genes, except for StALKBH2, were most highly expressed in the stolon and flower. Multiple hormone and stress-response elements were found to be located in the promoters of the StALKBH genes. Further qRT-PCR results suggest that they may be significantly upregulated in response to phytohormones and abiotic stress (except for cold), and the expression of most of the StALKBH genes exhibited positively modulated trends. Overall, this study is the first to report a genome-wide assessment of the ALKBH family in potato, providing valuable insights into candidate gene selection and facilitating in-depth functional analyses of ALKBH-mediated m6A methylation mechanisms in potato.

Emerging Orchestrator of Ecological Adaptation: m6A Regulation of Post-Transcriptional Mechanisms

Genetic mechanisms have been at the forefront of our exploration into the substrate of adaptive evolution and phenotypic diversification. However, genetic variation only accounts for a fraction of phenotypic variation. In the last decade, the significance of RNA modification mechanisms has become more apparent in the context of organismal adaptation to rapidly changing environments. RNA m6A methylation, the most abundant form of RNA modification, is emerging as a potentially significant player in various biological processes. Despite its fundamental function to regulate other major post-transcriptional mechanisms such as microRNA and alternative splicing, its role in ecology and evolution has been understudied. This review highlights the potential importance of m6A RNA methylation in ecological adaptation, emphasising the need for further research, especially in natural systems. We focus on how m6A not only affects mRNA fate but also influences miRNA-mediated gene regulation and alternative splicing, potentially contributing to organismal adaptation. The aim of this review is to synthesise key background information to enhance our understanding of m6A mechanisms driving species survival in dynamic environments and motivate future research into the dynamics of adaptive RNA methylation.

Detection, distribution, and functions of RNA N 6-methyladenosine (m6A) in plant development and environmental signal responses

The epitranscriptomic mark N 6-methyladenosine (m6A) is the most common type of messenger RNA (mRNA) post-transcriptional modification in eukaryotes. With the discovery of the demethylase FTO (FAT MASS AND OBESITY-ASSOCIATED PROTEIN) in Homo Sapiens, this modification has been proven to be dynamically reversible. With technological advances, research on m6A modification in plants also rapidly developed. m6A modification is widely distributed in plants, which is usually enriched near the stop codons and 3'-UTRs, and has conserved modification sequences. The related proteins of m6A modification mainly consist of three components: methyltransferases (writers), demethylases (erasers), and reading proteins (readers). m6A modification mainly regulates the growth and development of plants by modulating the RNA metabolic processes and playing an important role in their responses to environmental signals. In this review, we briefly outline the development of m6A modification detection techniques; comparatively analyze the distribution characteristics of m6A in plants; summarize the methyltransferases, demethylases, and binding proteins related to m6A; elaborate on how m6A modification functions in plant growth, development, and response to environmental signals; and provide a summary and outlook on the research of m6A in plants.

Quantitative profiling of m6A at single base resolution across the life cycle of rice and Arabidopsis

N6-methyladenosine (m6A) plays critical roles in regulating mRNA metabolism. However, comprehensive m6A methylomes in different plant tissues with single-base precision have yet to be reported. Here, we present transcriptome-wide m6A maps at single-base resolution in different tissues of rice and Arabidopsis using m6A-SAC-seq. Our analysis uncovers a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis. The evolutionarily conserved m6A sites in rice and Arabidopsis ortholog gene pairs are involved in controlling tissue development, photosynthesis and stress response. We observe an overall mRNA stabilization effect by 3' UTR m6A sites in certain plant tissues. Like in mammals, a positive correlation between the m6A level and the length of internal exons is also observed in plant mRNA, except for the last exon. Our data suggest an active m6A deposition process occurring near the stop codon in plant mRNA. In addition, the MTA-installed plant mRNA m6A sites correlate with both translation promotion and translation suppression, depicting a more complicated regulatory picture. Our results therefore provide in-depth resources for relating single-base resolution m6A sites with functions in plants and uncover a suppression-activation model controlling m6A biogenesis across species.

Principles, functions, and biological implications of m6A in plants

Over the past decade, N 6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression regulation, diverse physiologic and pathogenic processes, as well as crop trial implications, to guide discussions on challenges associated with and leveraging epitranscriptome editing for crop improvement.