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

Plant Communications, Journal Year: 2024, Volume and Issue: 5(10), P. 101037 - 101037

Published: July 6, 2024

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

Language: Английский

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Epigenetics in the modern era of crop improvements

Science China Life Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

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

Language: Английский

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Rational design of phytovirucide inhibiting nucleocapsid protein aggregation in tomato spotted wilt virus

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 27, 2025

Ineffectiveness of managing plant viruses by chemicals has posed serious challenges in crop production. Recently, phase separation shown to play a key role viral lifecycle. Using inhibitors that can disturb biomolecular condensates formed for virus control been reported medical field. However, the applicability this promising antiviral tactic protection not explored. Here, we report an inhibitor, Z9, targets tomato spotted wilt (TSWV) N protein. Z9 is capable interacting with amino acids nucleic acid binding region TSWV N, disrupting assembly and RNA into phase-separated condensates, reduction which detrimental stability This study provides strategy separation-based control. Biomolecular have recognized as crucial process life cycle. authors inhibitor targeting nucleocapsid protein (N) disrupt its potential

Language: Английский

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

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(12), P. 2586 - 2599

Published: Oct. 4, 2024

ABSTRACT Modifications to RNA have recently been recognized as a pivotal regulator of gene expression in living organisms. More than 170 chemical modifications identified RNAs, with N 6 ‐methyladenosine (m A) being the most abundant modification eukaryotic mRNAs. The addition and removal m A marks are catalyzed by methyltransferases (referred “writers”) demethylases “erasers”), respectively. In addition, mRNAs interpreted A‐binding proteins “readers”), which regulate fate mRNAs, including stability, splicing, transport, translation. Therefore, exploring mechanism underlying reader‐mediated modulation metabolism is essential for much deeper understanding epigenetic role plants. Recent discoveries improved our functions readers plant growth development, stress response, disease resistance. This review highlights latest developments reader research, emphasizing diverse RNA‐binding domains crucial function biological cellular roles response developmental environmental signals. Moreover, we propose discuss potential future research directions challenges identifying novel elucidating mechanistic

Language: Английский

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

Physiologia Plantarum, Journal Year: 2025, Volume and Issue: 177(1)

Published: Jan. 1, 2025

Abstract N6‐methyladenosine (m 6 A), the most prevalent modification found in eukaryotic mRNAs, is recognized and interpreted by m A‐binding proteins called A readers. The EVOLUTIONARILY CONSERVED C‐TERMINAL REGION (ECT) have increasingly been identified as readers plants. recent study has demonstrated that loss‐of‐function ect8 mutant sensitive to salt stress enhancing stability of negative regulators Arabidopsis ( thaliana ). In this study, we generated analyzed ECT8‐overexpressing transgenic plants further explore function ECT8 response. electrophoretic mobility shift assay vitro showed binds A‐modified synthetic RNAs, preferring UGUm AA UACm AGA motifs over GGm ACU motif. Contrary exhibiting hypersensitivity regulators, displayed tolerance increasing expression levels positive regulators. Moreover, RNA‐immunoprecipitation stress‐responsive mRNAs planta . Collectively, our current previous findings highlight ECT8‐mediated stabilization destabilization genes encoding or respectively, contribute Arabidopsis.

Language: Английский

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

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 142597 - 142597

Published: March 1, 2025

Language: Английский

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Phase separation as a key mechanism in plant development, environmental adaptation, and abiotic stress response

Journal of Biological Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 108548 - 108548

Published: April 1, 2025

Liquid-liquid phase separation is a fundamental biophysical process in which biopolymers, such as proteins, nucleic acids, and their complexes, spontaneously demix into distinct coexisting phases. This phenomenon drives the formation of membraneless organelles-cellular subcompartments without lipid bilayer that perform specialized functions. In plants, phase-separated biomolecular condensates play pivotal roles regulating gene expression, from genome organization to transcriptional post-transcriptional processes. addition, governs plant-specific traits, flowering photosynthesis. As sessile organisms, plants have evolved leverage for rapid sensing response environmental fluctuations stress conditions. Recent studies highlight critical role plant adaptation, particularly abiotic stress. review compiles latest research on biology, providing examples diverse functions development, responses. We propose represents conserved dynamic mechanism enabling adapt efficiently ever-changing Deciphering molecular mechanisms underlying responses opens new avenues biotechnological strategies aimed at engineering stress-resistant crops. These advancements significant implications agriculture, addressing crop productivity face climate change.

Language: Английский

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Detection, distribution, and functions of RNA N6-methyladenosine (m6A) in plant development and environmental signal responses

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: July 16, 2024

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

Language: Английский

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A Series of Novel Alleles of Ehd2 Modulating Heading and Salt Tolerance in Rice

Plants, Journal Year: 2025, Volume and Issue: 14(2), P. 297 - 297

Published: Jan. 20, 2025

Rice (Oryza sativa L.) is a staple crop for nearly half of the global population and one China’s most extensively cultivated cereals. Heading date, critical agronomic trait, determines regional seasonal adaptability rice varieties. In this study, series mutants (elh5 to elh12) exhibiting extremely late heading under both long-day (LD) short-day (SD) conditions were identified from an ethyl methanesulfonate (EMS) mutant library. Using MutMap map-based cloning, causative gene was as novel allele Ehd2/OsID1/RID1/Ghd10. Functional validation through CRISPR/Cas9 knockout complementation assays confirmed its role in regulating heading. The elh6 mutation found cause intron retention due alternative splicing. Ehd2 encodes Cys-2/His-2-type zinc finger transcription factor with IDD domain transcriptional activity yeast. Its expression peaks developing leaves before spikes during reproductive conversion. mutants, delayed resulted downregulating Ehd1-Hd3a pathway genes. Salinity stress significantly hampers growth productivity. Transcriptomic analysis elh10 ZH8015 seedlings exposed salt 24 h 5150 differentially expressed genes (DEGs) at seedling stage, predominantly linked response pathways. revealed modulator tolerance, likely regulation ion transport, enzyme activity, antioxidant systems. This study establishes pivotal promoting while negatively tolerance rice.

Language: Английский

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Strategies for RNA m6A modification application in crop improvement

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Oct. 15, 2024

The improvement of crop yield and quality is an eternal theme to face climate change population growth. key improving varieties lies in precisely manipulating gene expression. Recent advancements CRISPR/Cas9 technology have made knockout increasingly straightforward, yet for genes related important agronomic traits, it crucial regulate their expression levels appropriately. Complete often results defects other aspects. In addition, many traits require upregulation target improvement. Therefore, the development novel methods precise or downregulation expression, without altering protein sequences introducing new genome fragments, will significantly bolster technical foundation genetic improvement.N 6 -methyladenosine (m A) most abundant reversible internal chemical modification eukaryotic mRNA, which installed, removed, recognized by methyltransferases (writers), demethylases (erasers), m A-binding proteins (readers), respectively (Tang et al., 2023). Currently, two types A been identified plants: multiprotein complexes a single protein. complex includes MTA, MTB, FIP37, VIRILIZER (VIR), HAKAI, HIZ2 (HAKAI interacting zinc finger 2), catalyze majority modifications on mRNA (Parker 2021;Ruzicka 2017;Shen 2016;Zhang 2022;Zhong 2008). FIONA1 also exhibits methyltransferase activity Arabidopsis (Wang 2022;Xu 2022), catalyzing approximately 10% mRNA. Several demethylases, belong Fe (II)/α -kg dependent dioxygenase superfamily, plants, including AtALKBH10B AtALKBH9B, rice OsALKBH9, tomato SlALKBH2. Abinding proteins, such as ECTs Arabidopsis, contains YTH domain. ratio A/A poly + RNA varied among different tissues, with range 0.36-0.75% 0.52-0.67% rice, suggesting its high abundance 2024). At transcriptome level, sites are primarily enriched within 3′-untranslated region (3′ UTR), followed coding DNA sequence (CDS) 5′-untranslated (5′UTR). studies demonstrated roles regulating influencing stability, translation, 3′UTR processing Among them, stability regulation one primary functions A, involves aspects: acceleration decay preservation depending specific proteins. combining proteomics analysis shown that untranslated regions negatively correlated abundance, UTR likely inhibit plants. could lead increase (Li found play plant biology, embryo development, floral transition, stem cell fate determination, pollen fruit ripening, photomorphogenesis, circadian clock, nitrate signaling, responses biotic abiotic stress Given holds promise strategy enhancing traits.In mammals, demethylase FTO, known obesity gene, plays role body weight. Researchers genetically engineered potatoes express FTO. field experiments, biomass increased 50% (Yu 2021).Further research indicates FTO promotes root growth, tiller bud formation, photosynthetic efficiency, drought resistance, these phenotypes 2021).In strawberries, inhibiting FveMTA FveMTB can delay while upregulating either accelerate ripening time strawberries. (Zhou 2021). above suggests level overall enhance crops.In addition researchers endeavored edit individual genes. editing system has successfully developed fusing dCas13a core MTA-MTB mammalian ALKBH5 (Shi By specifically SHR transcript, was transcript promote enlargement aboveground parts leaf area, height, biomass, grain yield, thereby promoting growth cotton, similar tools developed, CRISPR/dCas13(Rx) GhMTA (Targeted Methylation Editor, TME) demethyltransferase GhALKBH10 Demethylation TDE) Using TME editor, GhDi19 increased, plants significant length enhanced resistance. Both works indicated phenotype improve traits.According current research, three strategies through modification. (1) Altering regulatory (RMRPs) (methyltransferases, recognition proteins) typically multitude substrate genes, this degree randomness uncertainty may frequently result phenotypic abnormalities; (2) Conducting Cas13 (dCas13) RNA-modified mRNA.However, RNA-based poses limitations breeding applications: vector must be maintained offspring, otherwise effect cannot preserved. they not suitable practical applications; (3) Alter remove modifications. For example, using base editor accurately replace Amodified adenine DNA. Regarding site UTR, employed disrupt motif eliminating This directly motifs DNA, enabling production materials transgenic vectors utilized applications.Steps 1: Draw single-base resolution map. purpose editing, accurate maps at generated initially. With detection technology, various sequencing reported, A-selective allyl labeling A-SAC-seq) (Hu Nanopore direct (DRS) (Zheng 2020) Glyoxal nitrite-mediated deamination unmethylated adenosine (GLORI-seq) (Liu 2022) broad application prospects (Figure 1).Recent reported transcriptome-wide tissues (plumule dark, plumule light, seedling 8 days, 2 weeks, panicle, flag 10 days after anthesis, endosperm anthesis) (seedling, shoot, root, rosette leaf, cauline stem, flower, silique, seed) A-SAC-seq, identifying total 205,691 distributed across 22,574 188,282 19,984 offering comprehensive resources investigating SAC-seq, DRS, GLORIseq, there no sequencing, crops constructed rapidly.Step2: Identification functional sites. Since more than ten thousand present transcriptome, ones remains question clarified. 1). ( 1 Utilizing RMRPs, several identified, STM WUS shoot (Shen 2016), FT, SPL3, SPL9 transition (Duan 2017), OsYUCCA3, TDR, GAMYB (Cheng 2022;Tang 2024), etc.In future, we should materials, comprehensively study under stages, environmental stimulation, pest disease field, explore Functional RMRPs. Interaction RMRPs might involved processes installing, removing, recognizing mRNAs. selection CRY2 recruits writer (MTA/MTB/FIP37) photobody blue clock associated (CCA1) OsFIP37 recruited RNA-binding OsFAP1 deposit OsYUCCA3 male germ miosis 2022). EARLY HEADING DATE6 (EHD6) reader YTH07 sequesters OsCOL4 into phase-separated ribonucleoprotein condensates, flowering (Cui 2024)Exploring dynamic mapping. mapping changes developmental stages same tissue, treatments crops, corresponding expected relevant functions.Step 3: editor. After generating map sites, screening positive seedlings, mutations, confirming changes, obtained Aedited Subsequently, conducted mutants, free screened subsequent breeding.Fine-tuning potential varieties. mRNAs, positioning tool advent methods, longer obstacle. limitation insufficient mining effective approach studying biological methyltransferases, binding response, processes. However, fewer so far, future strengthen identification summary, because vital post-transcriptionally,

Language: Английский

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