m6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis

RNA m6A modification meets plant hormones

Plant hormones are essential signalling molecules that control and coordinate diverse physiological processes in plant development and adaptation to ever-fluctuating environments. This hormonal regulation of plant development and environmental responses has recently been shown to extensively involve the most widespread RNA modification, N6-methyladenosine (m6A). Here we discuss the current understanding of the crosstalk between m6A and plant hormones, focusing on their reciprocal regulation, where hormonal signals induce m6A reprogramming and m6A affects hormone biosynthesis and signalling cascades. We also highlight new insights into how m6A contributes to the hormonal control of plant development and stress responses. Furthermore, we discuss future prospects for unveiling the regulatory networks that orchestrate epitranscriptome-hormone interactions and harnessing the related knowledge accrued to enhance crop productivity and resilience in changing environments.

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.

The transcriptional regulation of Arabidopsis ECT8 by ABA-Responsive Element binding transcription factors in response to ABA and abiotic stresses

N 6-methyladenosine modification is a critical epigenetic mark in the plant response to abscisic acid (ABA) and various abiotic stresses including salinity, drought, and cold stresses. Arabidopsis Evolutionarily Conserved C-Terminal Region 8 (ECT8), an m6A reader, has been reported to participate in the response to ABA and salinity stress. However, the intricate regulatory mechanisms governing ECT8 expression in these stress responses have not been fully elucidated. Our multidisciplinary analyses have revealed that ECT8 exhibits a broad expression pattern across tissues, with particularly high levels observed in senescent leaves. Furthermore, ECT8 expression is markedly upregulated in response to ABA, salinity, and osmotic stress. Intriguingly, the promoter region of the ECT8 gene harbors two ABA Responsive Elements (ABREs). Employing yeast one-hybrid assays, we identified that key ABRE-binding transcription factors within the ABA signaling cascade, namely ABA INSENSITIVE 5 (ABI5) and ABRE BINDING FACTOR1/2/3/4 (ABF1/2/3/4), exhibit a specific binding affinity for the ECT8 promoter, with the two ABREs indispensable for their interaction. The Dual-Luciferase Reporter assay and Chromatin immunoprecipitation assay confirmed their interaction in planta. The expression pattern of ECT8 in mutants deficient in the core components of the ABA signaling pathway indicated that ECT8 is modulated by ABI5/ABF-mediated ABA signaling. Collectively, our findings elucidate the feedback mechanism linking ABA perception to the regulation of ECT8 expression, thereby shedding new light on the intricate interplay between ABA signaling and RNA m6A modification. This discovery enriches our understanding of the molecular crosstalk that underpins plant stress responses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01565-7.

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.

Writers, readers, and erasers of N6-Methyladenosine (m6A) methylomes in oilseed rape: identification, molecular evolution, and expression profiling

BACKGROUND

m6A RNA modifications are the most prevalent internal modifications in eukaryotic mRNAs and are crucial for plant growth and development, as well as for responses to biotic or abiotic stresses. The modification is catalyzed by writers, removed by erasers, and decoded by various m6A-binding proteins, which are readers. Brassica napus is a major oilseed crop. The dynamic regulation of m6A modifications by writers, erasers, and readers offers potential targets for improving the quality of this crop.

RESULTS

In this study, we identified 92 m6A-regulatory genes in B. napus, including 13 writers, 29 erasers, and 50 readers. A phylogenetic analysis revealed that they could be further divided into four, three, and two clades, respectively. The distribution of protein motifs and gene structures among members of the same clade exhibited notable similarity. During the course of evolution, whole genome duplication (WGD) and segmental duplication were the primary drivers of the expansion of m6A-related gene families. The genes were subjected to rigorous purification selection. Additionally, several sites under positive selection were identified in the proteins. RNA-seq and quantitative real-time PCR (qRT-PCR) expression analyses revealed that the identified Bnam6As exhibit tissue-specific expression patterns, as well as their expression patterns in response to various abiotic and biotic stresses. The 2000 bp sequence upstream of Bnam6As contained a number of cis-acting elements that regulate plant growth and environmental response. Furthermore, the protein interaction network revealed their interactions with a number of proteins of significant functional importance.

CONCLUSION

The identification of m6A modifiers in oilseed rape and their molecular evolution and expression profiling have revealed potential functions and molecular mechanisms of m6A, thus establishing a foundation for further functional validation and molecular breeding.

Exploring ABI5 regulation: Post-translational control and cofactor interactions in ABA signaling

Abscisic acid insensitive 5 (ABI5) is a pivotal transcription factor in abscisic acid (ABA) signaling, playing an essential role in plant growth and responses to abiotic stress. This key regulator is subject to multifaceted regulation, especially on post-translational mechanisms. Recent research has shed light on the post-translational regulation of ABI5, encompassing both post-translational modifications (PTMs) and the modulation of its transcriptional activity. In this review, we provide a comprehensive overview of the current knowledge surrounding the post-translational regulation of ABI5, along with the influence of various cofactors on its transcriptional activity and protein stability. The potential biological roles of PTMs of ABI5 in the context of ABA signaling and plant stress responses are also explored. As ABI5 is one of the most extensively studied proteins in the context of plant ABA signaling and environmental stress responses, a sophisticated and precise understanding of the regulatory mechanisms that govern ABI5 is not only beneficial for its application in genetic engineering but also helpful for our exploration in the fundamental principles of post-translational regulation.

Impact of UV-Irradiated Mesoporous Titania Nanoparticles (mTiNPs) on Key Onco- and Tumor Suppressor microRNAs of PC3 Prostate Cancer Cells

BACKGROUND

Mesoporous titanium dioxide nanoparticles (mTiNPs) are known for their chemical stability, non-toxicity, antimicrobial and anticancer effects, as well as for their photocatalytic properties. When this material is subjected to UV radiation, its electronic structure shifts, and during that process, reactive oxygen species are generated, which in turn exert apoptotic events on the cancer cells.

OBJECTIVES

We evaluated the cytotoxic effects of UV-irradiated mTiNPs on prostate cancer (PCa) cell line PC3 with the aim of demonstrating that the interaction between UV-light and mTiNPs positively impacts the nanomaterial's cytotoxic efficiency. Moreover, we assessed the differential expression of key oncomiRs and tumor suppressor (TS) miRNAs, as well as their associated target genes, in cells undergoing this treatment.

METHODS

PBS-suspended mTiNPs exposed to 290 nm UV light were added at different concentrations to PC3 cells. Cell viability was determined after 24 h with a crystal violet assay. Then, the obtained IC50 concentration of UV-nanomaterial was applied to a new PC3 cell culture, and the expression of a set of miRNAs and selected target genes was evaluated via qRT-PCR.

RESULTS

The cells exposed to photo-activated mTiNPs required 4.38 times less concentration of the nanomaterial than the group exposed to non-irradiated mTiNPs to achieve the half-maximal inhibition, demonstrating an improved cytotoxic performance of the UV-irradiated mTiNPs. Moreover, the expression of miR-18a-5p, miR-21-5p, and miR-221-5p was downregulated after the application of UV-mTiNPs, while TS miR-200a-5p and miR-200b-5p displayed an upregulated expression. Among the miRNA target genes, PTEN was found to be upregulated after the treatment, while BCL-2 and TP53 were underexpressed.

CONCLUSIONS

Our cytotoxic outcomes coincided with previous reports performed in other cancer cell lines, strongly suggesting UV-irradiated mTiNPs as a promising nano-therapeutic approach against PCa. On the other hand, to the best of our knowledge, this is the first report exploring the impact of UV-irradiated mTiNPs on key onco- and TS microRNAs in PCa cells.

Comprehensive analysis of epigenetic modifications in alfalfa under cadmium stress

Epigenetics plays an important role in plant growth and development and in environmental adaptation. Alfalfa, an important forage crop, is rich in nutrients. However, little is known about the molecular regulatory mechanisms underlying the response of alfalfa to cadmium (Cd) stress. Here, we performed DNA methylation (5mC), RNA methylation (m6A) and transcriptomic sequencing analyses of alfalfa roots under Cd stress. Whole-genome methylation sequencing and transcriptomic sequencing revealed that Cd stress reduced DNA methylation levels. Moreover, a reduced 5mC methylation level was associated with decreased expression of several DNA methyltransferase genes. Compared with those under normal (CK) conditions, the m6A modification levels under Cd stress were greater and were positively correlated with gene expression in alfalfa roots. We also found a negative correlation between the 5mC level and the m6A level, especially in CG and CHG contexts. In yeast, the overexpression of MsNARMP5 (natural resistance-associated macrophage protein) and MsPCR2 (plant cadmium resistance 2), which are modified by 5mC or m6A, significantly increased Cd stress tolerance. These results provide candidate genes for future studies on the mechanism of Cd stress tolerance in alfalfa roots and valuable information for studying heavy metal stress in alfalfa breeding.

Epigenetics in the modern era of crop improvements

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

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.

RNA Metabolism and the Role of Small RNAs in Regulating Multiple Aspects of RNA Metabolism

RNA metabolism is focused on RNA molecules and encompasses all the crucial processes an RNA molecule may or will undergo throughout its life cycle. It is an essential cellular process that allows all cells to function effectively. The transcriptomic landscape of a cell is shaped by the processes such as RNA biosynthesis, maturation (RNA processing, folding, and modification), intra- and inter-cellular transport, transcriptional and post-transcriptional regulation, modification, catabolic decay, and retrograde signaling, all of which are interconnected and are essential for cellular RNA homeostasis. In eukaryotes, sRNAs, typically 20-31 nucleotides in length, are a class of ncRNAs found to function as nodes in various gene regulatory networks. sRNAs are known to play significant roles in regulating RNA population at the transcriptional, post-transcriptional, and translational levels. Along with sRNAs, such as miRNAs, siRNAs, and piRNAs, new categories of ncRNAs, i.e., lncRNAs and circRNAs, also contribute to RNA metabolism regulation in eukaryotes. In plants, various genetic screens have demonstrated that sRNA biogenesis mutants, as well as RNA metabolism pathway mutants, exhibit similar growth and development defects, misregulated primary and secondary metabolism, as well as impaired stress response. In addition, sRNAs are both the "products" and the "regulators" in broad RNA metabolism networks; gene regulatory networks involving sRNAs form autoregulatory loops that affect the expression of both sRNA and the respective target. This review examines the interconnected aspects of RNA metabolism with sRNA regulatory pathways in plants. It also explores the potential conservation of these pathways across different kingdoms, particularly in plants and animals. Additionally, the review highlights how cellular RNA homeostasis directly impacts adaptive responses to environmental changes as well as different developmental aspects in plants.

Genome-Wide Identification and Expression Analysis of Members in the YT521-B Homology Domain-Containing RNA Binding Protein Family in Ginkgo biloba

N6-methyladenosine (m6A) is a widespread post-transcriptional modification of RNA in eukaryotes. The conserved YTH-domain-containing RNA binding protein has been widely reported to serve as a typical m6A reader in various species. However, no studies have reported the m6A readers in Ginkgo biloba (G. biloba). In this study, a systematic analysis of the m6A reader (YTH) gene family was performed on G. biloba, identifying 10 YTH genes in its genome. Phylogenetic analysis of protein-coding sequences revealed that YTH genes from G. biloba could be classified into two subgroups: GbDC1 and GbDC2 in GbDC and GbDF1-8 in GbDF, each with similar motifs and gene structures. In G. biloba, the predicated aromatic cage pocket of the YTH domains in the YTH gene family is uniformly composed of tryptophan residues (WWW). Subcellular localization experiments verified that GbDC1 is indeed localized in the nucleus, while GbDF1 is localized in both the nucleus and the cytoplasm. The expression patterns of the identified m6A reader genes showed a wide distribution but were tissue-specific. Most genes were highly expressed in leaves, followed by the stem, while the lowest expression tendency was found in the roots. Cis-regulatory element analysis predicted the possible functions of YTH genes in G. biloba, which were mainly responsive to plant hormones such as ABA and MeJA, as well as stress responses. Furthermore, the expression levels of YTH genes indeed changed significantly after ABA, MeJA, and NaCl treatments, suggesting that they can be affected by these abiotic factors. In addition, the PLAAC prediction results indicate that prion domains exist in GbDF1, GbDF2, GbDF3, GbDF4, GbDF6, GbDF7, GbDF8, and GbDC1, and phase separation is possible. This study provides a foundation for further investigation of the effects of m6A methylation on gene expression regulation in G. biloba and other forest trees.

An mRNA methylase and demethylase regulate sorghum salt tolerance by mediating N6-methyladenosine modification

N 6-methyladenosine (m6A) modification is a crucial and widespread molecular mechanism governing plant development and stress tolerance. The specific impact of m6A regulation on plants with inherently high salt tolerance remains unclear. Existing research primarily focuses on the overexpression or knockout of individual writer or eraser components to alter m6A levels. However, a comprehensive study simultaneously altering overall m6A modification levels within the same experiment is lacking. Such an investigation is essential to determine whether opposing changes in m6A modification levels exert entirely different effects on plant salt tolerance. In this study, we identified the major writer member mRNA adenosine methylase A (SbMTA) in sorghum (Sorghum bicolor) as critical for sorghum survival. The sbmta mutant exhibits a phenotype characterized by reduced overall m6A, developmental arrest, and, ultimately, lethality. Overexpression of SbMTA increased m6A levels and salt tolerance, while overexpression of the m6A eraser alkylated DNA repair protein AlkB homolog 10B (SbALKBH10B) in sorghum showed the opposite phenotype. Comparative analyses between sorghum with different m6A levels reveal that SbMTA- and SbALKBH10B-mediated m6A alterations significantly impact the stability and expression levels of genes related to the abscisic acid signaling pathway and growth under salt stress. In summary, this study unveils the intricate relationship between m6A modifications and salt tolerance in sorghum, providing valuable insights into how m6A modification levels on specific transcripts influence responses to salt stress.

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.

The m6A-YTH regulatory system in plants: A status

Plants use mRNA methylation to regulate gene expression. As in other eukaryotes, the only abundant methylated nucleotide in plant mRNA bodies is N6-methyladenosine (m6A). The conserved core components of m6A-based genetic control are a multi-subunit nuclear methyltransferase, and a set of nuclear and cytoplasmic RNA-binding proteins consisting of an m6A recognition module, the YT521-B homology (YTH) domain, and long intrinsically disordered regions (IDRs). In plants, this system is essential for growth during embryonic and post-embryonic development, but emerging evidence also points to key functions in plant-virus interactions and stimulus-dependent gene regulation. Cytoplasmic YTH-domain proteins are particularly important for these functions, and recent progress has identified two elements of the underlying molecular mechanisms: IDR-mediated phase separation and conserved short linear motifs mediating interactions with other key mRNA-binding proteins.

ALBA proteins facilitate cytoplasmic YTHDF-mediated reading of m6A in Arabidopsis

N6-methyladenosine (m6A) exerts many of its regulatory effects on eukaryotic mRNAs by recruiting cytoplasmic YT521-B homology-domain family (YTHDF) proteins. Here, we show that in Arabidopsis thaliana, the interaction between m6A and the major YTHDF protein ECT2 also involves the mRNA-binding ALBA protein family. ALBA and YTHDF proteins physically associate via a deeply conserved short linear motif in the intrinsically disordered region of YTHDF proteins and their mRNA target sets overlap, with ALBA4 binding sites being juxtaposed to m6A sites. These binding sites correspond to pyrimidine-rich elements previously found to be important for m6A binding to ECT2. Accordingly, both the biological functions of ECT2, and its binding to m6A targets in vivo, require ALBA association. Our results introduce the YTHDF-ALBA complex as the functional cytoplasmic m6A-reader in Arabidopsis, and define a molecular foundation for the concept of facilitated m6A reading, which increases the potential for combinatorial control of biological m6A effects.

Selective recognition of PTRE1 transcripts mediated by protein-protein interaction between the m6A reader ECT2 and PTRE1

N6-methyladenosine (m6A) is a prevalent internal post-transcriptional modification in eukaryotic RNAs executed by m6A-binding proteins known as "readers." Our previous research demonstrated that the Arabidopsis m6A reader ECT2 positively regulates transcript levels of the proteasome regulator PTRE1 and several 20S proteasome subunits, thereby enhancing 26S proteasome activity. However, mechanism underlying the selective recognition of m6A targets by readers, such as ECT2, remains elusive. In this study, we further demonstrate that ECT2 physically interacts with PTRE1 and several 20S proteasome subunits. This interaction, which occurs on the ribosome, involves the N terminus of PTRE1, suggesting that ECT2 might bind to the nascent PTRE1 polypeptide. Deleting ECT2's protein interaction domain impairs its mRNA-binding ability, whereas mutations in the m6A-RNA-binding site do not affect protein-protein interactions. Moreover, introducing a novel protein-binding domain into ECT2 increases transcript levels of proteins interacting with this domain. Our findings indicate that interaction with the PTRE1 protein enhances ECT2's binding to PTRE1 m6A mRNAs during translation, thereby regulating PTRE1 mRNA levels.

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.

Methyltransferase ATMETTL5 writes m6A on 18S ribosomal RNA to regulate translation in Arabidopsis

Aberrant RNA modifications can lead to dysregulated gene expression and impeded growth in plants. Ribosomal RNA (rRNA) constitutes a substantial portion of total RNA, while the precise functions and molecular mechanisms underlying rRNA modifications in plants remain largely elusive. Here, we elucidated the exclusive occurrence of the canonical RNA modification N6-methyladenosine (m6A) solely 18S rRNA, but not 25S rRNA. We identified a completely uncharacterized protein, ATMETTL5, as an Arabidopsis m6A methyltransferase responsible for installing m6A methylation at the 1771 site of the 18S rRNA. ATMETTL5 is ubiquitously expressed and localized in both nucleus and cytoplasm, mediating rRNA m6A methylation. Mechanistically, the loss of ATMETTL5-mediated methylation results in attenuated translation. Furthermore, we uncovered the role of ATMETTL5-mediated methylation in coordinating blue light-mediated hypocotyl growth by regulating the translation of blue light-related messenger RNAs (mRNAs), specifically HYH and PRR9. Our findings provide mechanistic insights into how rRNA modification regulates ribosome function in mRNA translation and the response to blue light, thereby advancing our understanding of the role of epigenetic modifications in precisely regulating mRNA translation in plants.

Phosphate deficiency alters transcript isoforms via alternative transcription start sites

Alternative transcription start sites (TSS) are widespread in eukaryotes and can alter the 5' UTR length and coding potential of transcripts. Here we show that inorganic phosphate (Pi) availability regulates the usage of several alternative TSS in Arabidopsis (Arabidopsis thaliana). In comparison to phytohormone treatment, Pi had a pronounced and specific effect on the usage of many alternative TSS. By combining short-read RNA sequencing with long-read sequencing of full-length mRNAs, we identified a set of 45 genes showing alternative TSS under Pi deficiency. Alternative TSS affected several processes, such as translation via the exclusion of upstream open reading frames present in the 5' UTR of RETICULAN LIKE PROTEIN B1 mRNA, and subcellular localization via removal of the plastid transit peptide coding region from the mRNAs of HEME OXYGENASE 1 and SULFOQUINOVOSYLDIACYLGLYCEROL 2. Several alternative TSS also generated shorter transcripts lacking the coding potential for important domains. For example, the EVOLUTIONARILY CONSERVED C-TERMINAL REGION 4 (ECT4) locus, which encodes an N6-methyladenosine (m6A) reader, strongly expressed under Pi deficiency a short noncoding transcript (named ALTECT4) ~550 nt long with a TSS in the penultimate intron. The specific and robust induction of ALTECT4 production by Pi deficiency led to the identification of a role for m6A readers in primary root growth in response to low phosphate that is dependent on iron and is involved in modulating cell division in the root meristem. Our results identify alternative TSS usage as an important process in the plant response to Pi deficiency.

Spatially heterogeneous selection and inter-varietal differentiation maintain population structure and local adaptation in a widespread conifer

BACKGROUND

Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) plays a critical role in the ecology and economy of Western North America. This conifer species comprises two distinct varieties: the coastal variety (var. menziesii) along the Pacific coast, and the interior variety (var. glauca) spanning the Rocky Mountains into Mexico, with instances of inter-varietal hybridization in Washington and British Columbia. Recent investigations have focused on assessing environmental pressures shaping Douglas-fir's genomic variation for a better understanding of its evolutionary and adaptive responses. Here, we characterize range-wide population structure, estimate inter-varietal hybridization levels, identify candidate loci for climate adaptation, and forecast shifts in species and variety distribution under future climates.

RESULTS

Using a custom SNP-array, we genotyped 540 trees revealing four distinct clusters with asymmetric admixture patterns in the hybridization zone. Higher genetic diversity observed in coastal and hybrid populations contrasts with lower diversity in inland populations of the southern Rockies and Mexico, exhibiting a significant isolation by distance pattern, with less marked but still significant isolation by environment. For both varieties, we identified candidate loci associated with local adaptation, with hundreds of genes linked to processes such as stimulus response, reactions to chemical compounds, and metabolic functions. Ecological niche modeling revealed contrasting potential distribution shifts among the varieties in the coming decades, with interior populations projected to lose habitat and become more vulnerable, while coastal populations are expected to gain suitable areas.

CONCLUSIONS

Overall, our findings provide crucial insights into the population structure and adaptive potential of Douglas-fir, with the coastal variety being the most likely to preserve its evolutionary path throughout the present century, which carry implications for the conservation and management of this species across their range.

m6A modification plays an integral role in mRNA stability and translation during pattern-triggered immunity

Plants employ distinct mechanisms to respond to environmental changes. Modification of mRNA by N 6-methyladenosine (m6A), known to affect the fate of mRNA, may be one such mechanism to reprogram mRNA processing and translatability upon stress. However, it is difficult to distinguish a direct role from a pleiotropic effect for this modification due to its prevalence in RNA. Through characterization of the transient knockdown-mutants of m6A writer components and mutants of specific m6A readers, we demonstrate the essential role that m6A plays in basal resistance and pattern-triggered immunity (PTI). A global m6A profiling of mock and PTI-induced Arabidopsis plants as well as formaldehyde fixation and cross-linking immunoprecipitation-sequencing of the m6A reader, EVOLUTIONARILY CONSERVED C-TERMINAL REGION2 (ECT2) showed that while dynamic changes in m6A modification and binding by ECT2 were detected upon PTI induction, most of the m6A sites and their association with ECT2 remained static. Interestingly, RNA degradation assay identified a dual role of m6A in stabilizing the overall transcriptome while facilitating rapid turnover of immune-induced mRNAs during PTI. Moreover, polysome profiling showed that m6A enhances immune-associated translation by binding to the ECT2/3/4 readers. We propose that m6A plays a positive role in plant immunity by destabilizing defense mRNAs while enhancing their translation efficiency to create a transient surge in the production of defense proteins.

The m6A reader ECT8 is an abiotic stress sensor that accelerates mRNA decay in Arabidopsis

N 6-methyladenosine (m6A) is the most abundant mRNA modification and plays diverse roles in eukaryotes, including plants. It regulates various processes, including plant growth, development, and responses to external or internal stress responses. However, the mechanisms underlying how m6A is related to environmental stresses in both mammals and plants remain elusive. Here, we identified EVOLUTIONARILY CONSERVED C-TERMINAL REGION 8 (ECT8) as an m6A reader protein and showed that its m6A-binding capability is required for salt stress responses in Arabidopsis (Arabidopsis thaliana). ECT8 accelerates the degradation of its target transcripts through direct interaction with the decapping protein DECAPPING 5 within processing bodies. We observed a significant increase in the ECT8 expression level under various environmental stresses. Using salt stress as a representative stressor, we found that the transcript and protein levels of ECT8 rise in response to salt stress. The increased abundance of ECT8 protein results in the enhanced binding capability to m6A-modified mRNAs, thereby accelerating their degradation, especially those of negative regulators of salt stress responses. Our results demonstrated that ECT8 acts as an abiotic stress sensor, facilitating mRNA decay, which is vital for maintaining transcriptome homeostasis and enhancing stress tolerance in plants. Our findings not only advance the understanding of epitranscriptomic gene regulation but also offer potential applications for breeding more resilient crops in the face of rapidly changing environmental conditions.

Transcriptome-Wide Identification of m6A Writers, Erasers and Readers and Their Expression Profiles under Various Biotic and Abiotic Stresses in Pinus massoniana Lamb

N6-methyladenosine (m6A) RNA modification is the most prevalent form of RNA methylation and plays a crucial role in plant development. However, our understanding of m6A modification in Masson pine (Pinus massoniana Lamb.) remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in Masson pine was performed, and 22 m6A regulatory genes were identified in total, including 7 m6A writers, 7 m6A erases, and 8 readers. Phylogenetic analysis revealed that all m6A regulators involved in Masson pine could be classified into three distinct groups based on their domains and motifs. The tissue expression analysis revealed that the m6A regulatory gene may exert a significant influence on the development of reproductive organs and leaves in Masson pine. Moreover, the results from stress and hormone expression analysis indicated that the m6A regulatory gene in Masson pine might be involved in drought stress response, ABA-signaling-pathway activation, as well as resistance to Monochamus alternatus. This study provided valuable and anticipated insights into the regulatory genes of m6A modification and their potential epigenetic regulatory mechanisms in Masson pine.

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.

The m6A reader SlYTH2 negatively regulates tomato fruit aroma by impeding the translation process

N6-methyladenosine (m6A) is a fundamentally important RNA modification for gene regulation, whose function is achieved through m6A readers. However, whether and how m6A readers play regulatory roles during fruit ripening and quality formation remains unclear. Here, we characterized SlYTH2 as a tomato m6A reader protein and profiled the binding sites of SlYTH2 at the transcriptome-wide level. SlYTH2 undergoes liquid-liquid phase separation and promotes RNA-protein condensate formation. The target mRNAs of SlYTH2, namely m6A-modified SlHPL and SlCCD1B associated with volatile synthesis, are enriched in SlYTH2-induced condensates. Through polysome profiling assays and proteomic analysis, we demonstrate that knockout of SlYTH2 expedites the translation process of SlHPL and SlCCD1B, resulting in augmented production of aroma-associated volatiles. This aroma enrichment significantly increased consumer preferences for CRISPR-edited fruit over wild type. These findings shed light on the underlying mechanisms of m6A in plant RNA metabolism and provided a promising strategy to generate fruits that are more attractive to consumers.

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.

RNA m6A modification facilitates DNA methylation during maize kernel development

N6-methyladenosine (m6A) in mRNA and 5-methylcytosine (5mC) in DNA have critical functions for regulating gene expression and modulating plant growth and development. However, the interplay between m6A and 5mC is an elusive territory and remains unclear mechanistically in plants. We reported an occurrence of crosstalk between m6A and 5mC in maize (Zea mays) via the interaction between mRNA adenosine methylase (ZmMTA), the core component of the m6A methyltransferase complex, and decrease in DNA methylation 1 (ZmDDM1), a key chromatin-remodeling factor that regulates DNA methylation. Genes with m6A modification were coordinated with a much higher level of DNA methylation than genes without m6A modification. Dysfunction of ZmMTA caused severe arrest during maize embryogenesis and endosperm development, leading to a significant decrease in CHH methylation in the 5' region of m6A-modified genes. Instead, loss of function of ZmDDM1 had no noteworthy effects on ZmMTA-related activity. This study establishes a direct link between m6A and 5mC during maize kernel development and provides insights into the interplay between RNA modification and DNA methylation.

A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.

A YTHDF-PABP interaction is required for m6 A-mediated organogenesis in plants

N6-methyladenosine (m6 A) in mRNA is key to eukaryotic gene regulation. Many m6 A functions involve RNA-binding proteins that recognize m6 A via a YT521-B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. The Arabidopsis thaliana YTH domain proteins ECT2, ECT3, and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we use ECT2 to reveal molecular underpinnings of this function. We show that stimulation of leaf formation requires the long N-terminal IDR, and we identify two short IDR elements required for ECT2-mediated organogenesis. Of these two, a 19-amino acid region containing a tyrosine-rich motif conserved in both plant and metazoan YTHDF proteins is necessary for binding to the major cytoplasmic poly(A)-binding proteins PAB2, PAB4, and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation in ect2 ect3 ect4 mutants, suggesting that the ECT2-PAB2/4/8 interaction on target mRNAs of organogenesis-related genes may overcome limiting PAB concentrations in primordial cells.

Genome-Wide Identification and Characterization of the YTH Domain-Containing RNA-Binding Protein Family in Liriodendron chinense

N6-methyladenosine (m6A) is becoming one of the most important RNA modifications in plant growth and development, including defense, cell differentiation, and secondary metabolism. YT521-B homology (YTH) domain-containing RNA-binding proteins, identified as m6A readers in epitranscriptomics, could affect the fate of m6A-containing RNA by recognizing and binding the m6A site. Therefore, the identification and study of the YTH gene family in Liriodendron chinense (L. chinense) can provide a molecular basis for the study of the role of m6A in L. chinense, but studies on the YTH gene in L. chinense have not been reported. We identified nine putative YTH gene models in the L. chinense genome, which can be divided into DF subgroups and DC subgroups. Domain sequence analysis showed that the LcYTH protein had high sequence conservation. A LcYTH aromatic cage bag is composed of tryptophan and tryptophan (WWW). PrLDs were found in the protein results of YTH, suggesting that these genes may be involved in the process of liquid-liquid phase separation. LcYTH genes have different tissue expression patterns, but the expression of LcYTHDF2 is absolutely dominant in all tissues. In addition, the expression of the LcYTH genes is changed in response to ABA and MeJA. In this study, We identified and analyzed the expression pattern of LcYTH genes. Our results laid a foundation for further study of the function of the LcYTH gene and further genetic and functional analyses of m6A RNA modification in forest trees.

Insights into the conservation and diversification of the molecular functions of YTHDF proteins

YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A) in mRNA. Members of the YTHDF clade determine properties of m6A-containing mRNAs in the cytoplasm. Vertebrates encode three YTHDF proteins whose possible functional specialization is debated. In land plants, the YTHDF clade has expanded from one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain placed behind a long N-terminal intrinsically disordered region (IDR). ECT2, ECT3 and ECT4 show genetic redundancy in stimulation of primed stem cell division, but the origin and implications of YTHDF expansion in higher plants are unknown, as it is unclear whether it involves acquisition of fundamentally different molecular properties, in particular of their divergent IDRs. Here, we use functional complementation of ect2/ect3/ect4 mutants to test whether different YTHDF proteins can perform the same function when similarly expressed in leaf primordia. We show that stimulation of primordial cell division relies on an ancestral molecular function of the m6A-YTHDF axis in land plants that is present in bryophytes and is conserved over YTHDF diversification, as it appears in all major clades of YTHDF proteins in flowering plants. Importantly, although our results indicate that the YTH domains of all arabidopsis ECT proteins have m6A-binding capacity, lineage-specific neo-functionalization of ECT1, ECT9 and ECT11 happened after late duplication events, and involves altered properties of both the YTH domains, and, especially, of the IDRs. We also identify two biophysical properties recurrent in IDRs of YTHDF proteins able to complement ect2 ect3 ect4 mutants, a clear phase separation propensity and a charge distribution that creates electric dipoles. Human and fly YTHDFs do not have IDRs with this combination of properties and cannot replace ECT2/3/4 function in arabidopsis, perhaps suggesting different molecular activities of YTHDF proteins between major taxa.

The emerging role of epitranscriptome in shaping stress responses in plants

KEY MESSAGE

RNA modifications and editing changes constitute 'epitranscriptome' and are crucial in regulating the development and stress response in plants. Exploration of the epitranscriptome and associated machinery would facilitate the engineering of stress tolerance in crops. RNA editing and modifications post-transcriptionally decorate almost all classes of cellular RNAs, including tRNAs, rRNAs, snRNAs, lncRNAs and mRNAs, with more than 170 known modifications, among which m6A, Ψ, m5C, 8-OHG and C-to-U editing are the most abundant. Together, these modifications constitute the "epitranscriptome", and contribute to changes in several RNA attributes, thus providing an additional structural and functional diversification to the "cellular messages" and adding another layer of gene regulation in organisms, including plants. Numerous evidences suggest that RNA modifications have a widespread impact on plant development as well as in regulating the response of plants to abiotic and biotic stresses. High-throughput sequencing studies demonstrate that the landscapes of m6A, m5C, Am, Cm, C-to-U, U-to-G, and A-to-I editing are remarkably dynamic during stress conditions in plants. GO analysis of transcripts enriched in Ψ, m6A and m5C modifications have identified bonafide components of stress regulatory pathways. Furthermore, significant alterations in the expression pattern of genes encoding writers, readers, and erasers of certain modifications have been documented when plants are grown in challenging environments. Notably, manipulating the expression levels of a few components of RNA editing machinery markedly influenced the stress tolerance in plants. We provide updated information on the current understanding on the contribution of RNA modifications in shaping the stress responses in plants. Unraveling of the epitranscriptome has opened new avenues for designing crops with enhanced productivity and stress resilience in view of global climate change.