Strategies for RNA m6A modification application in crop improvement DOI Creative Commons
Jun Tang,

Xuemin Wang

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

Molecular innovations in plant TIR-based immunity signaling DOI Creative Commons
Dmitry Lapin, Oliver Johanndrees, Zhongshou Wu

et al.

The Plant Cell, Journal Year: 2022, Volume and Issue: 34(5), P. 1479 - 1496

Published: Feb. 4, 2022

Abstract A protein domain (Toll and Interleukin-1 receptor [TIR]-like) with homology to animal TIRs mediates immune signaling in prokaryotes eukaryotes. Here, we present an overview of TIR evolution the molecular versatility domains different architectures for host protection against microbial attack. Plant TIR-based emerges as being central potentiation effectiveness defenses triggered by intracellular cell-surface receptors. Equally relevant plant fitness are mechanisms that limit potent healthy tissues but maintain preparedness infection. We propose seed plants evolved a specialized module selectively translate enzymatic activities defense outputs, overlaying more general function TIRs.

Language: Английский

Citations

76
Two zinc finger proteins with functions in m6A writing interact with HAKAI DOI Creative Commons
Mi Zhang, Zsuzsanna Bódi,

Katarzyna Mackinnon

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 2, 2022

Abstract The methyltransferase complex (m 6 A writer), which catalyzes the deposition of N -methyladenosine A) in mRNAs, is highly conserved across most eukaryotic organisms, but its components and interactions between them are still far from fully understood. Here, using vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 HIZ2, discovered as Arabidopsis m writer complex. HAKAI required for MTA (mRNA adenosine methylase A). Whilst knockout plants have normal levels A, it overexpressed show reduced methylation decreased lateral root formation. Mutant lacking HIZ2 viable an 85% reduction abundance severe developmental defects. Our findings suggest that likely plant equivalent ZC3H13 (Flacc) metazoan A-METTL Associated Complex.

Language: Английский

Citations

73
Detection, regulation, and functions of RNA N6-methyladenosine modification in plants DOI Creative Commons
Jun Tang, Shuyan Chen,

Guifang Jia

et al.

Plant Communications, Journal Year: 2023, Volume and Issue: 4(3), P. 100546 - 100546

Published: Jan. 10, 2023

N6-Methyladenosine (m6A) is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles gene expression regulation, including transcriptional post-transcriptional regulation. m6A a reversible that installed, removed, recognized by methyltransferases (writers), demethylases (erasers), m6A-binding proteins (readers), respectively. Recently, breadth of research on plants has expanded, vital plant development, biotic abiotic stress responses, crop trait improvement have been investigated. In this review, we discuss recent developments highlight detection methods, distribution, regulatory proteins, molecular biological functions plants. We also offer some perspectives future investigations, providing direction for subsequent

Language: Английский

Citations

53
A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis DOI Creative Commons
Runxuan Zhang, Richard Kuo, Max Coulter

et al.

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: July 7, 2022

Accurate and comprehensive annotation of transcript sequences is essential for quantification differential gene expression analysis. Single-molecule long-read sequencing technologies provide improved integrity structures including alternative splicing, transcription start polyadenylation sites. However, accuracy significantly affected by errors, mRNA degradation, or incomplete cDNA synthesis.We present a new Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts-twice that the best current transcriptome 1500 novel genes. Seventy-eight percent transcripts are from Iso-seq with accurately defined splice junctions end We develop methods to determine sites accurately. Mismatch profiles around powerful feature distinguish correct remove false junctions. Stratified approaches identify high-confidence fragmentary due degradation. major improvement existing transcriptomes as demonstrated analysis an cold response RNA-seq time-series. provides higher resolution profiling identifies cold-induced site usage.AtRTD3 most currently. It improves precision expression, start/end usage data. The identifying accurate widely applicable will improve single-molecule any species.

Language: Английский

Citations

68
m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5’ splice site DOI Creative Commons
Matthew T Parker, Beth K Soanes,

Jelena Kusakina

et al.

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Nov. 21, 2022

Alternative splicing of messenger RNAs is associated with the evolution developmentally complex eukaryotes. Splicing mediated by spliceosome, and docking pre-mRNA 5’ splice site into spliceosome active depends upon pairing conserved ACAGA sequence U6 snRNA. In some species, including humans, central adenosine AC A GA box modified N 6 methylation, but role this m modification poorly understood. Here, we show that snRNA determines accuracy efficiency splicing. We reveal methyltransferase, FIONA1, required for Arabidopsis modification. fio1 mutants disrupted patterns can be explained composition sites cooperative roles U5 in selection. influences 3’ usage. generalise these findings to two major classes diverse eukaryotes, which display anti-correlated interaction potential loop 1 box. conclude contributes selection degenerate crucial alternative

Language: Английский

Citations

41
Recent advances in the plant epitranscriptome DOI Creative Commons
Lisha Shen, Jinqi Ma, Ping Li

et al.

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: March 7, 2023

Abstract Chemical modifications of RNAs, known as the epitranscriptome, are emerging widespread regulatory mechanisms underlying gene regulation. The field epitranscriptomics advances recently due to improved transcriptome-wide sequencing strategies for mapping RNA and intensive characterization writers, erasers, readers that deposit, remove, recognize modifications, respectively. Herein, we review recent in characterizing plant epitranscriptome its post-transcriptional regulation diverse physiological processes, with main emphasis on N 6 -methyladenosine (m A) 5-methylcytosine 5 C). We also discuss potential challenges utilization editing crop improvement.

Language: Английский

Citations

34
An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length DOI
Jinbu Jia, Wenqin Lu, Bo Liu

et al.

Nature Plants, Journal Year: 2022, Volume and Issue: 8(9), P. 1118 - 1126

Published: Aug. 18, 2022

Language: Английский

Citations

30
Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana DOI Creative Commons
Jérémy Berthelier, Leonardo Furci, Shuta Asai

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: June 5, 2023

Abstract Transposable elements (TEs) are accumulated in both intergenic and intragenic regions plant genomes. Intragenic TEs often act as regulatory of associated genes also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation gene function, prevalence transcriptional transcripts poorly understood. By long-read direct RNA sequencing a dedicated bioinformatics pipeline, ParasiTE, we investigated transcription processing Arabidopsis thaliana . We identified global production thousands A. loci, TE sequences being alternative start sites or termination sites. The epigenetic state affects RNAPII elongation usage poly(A) signals within sequences, regulating isoform production. Co-transcription inclusion TE-derived into stability environmental responses some loci. Our study provides insights interactions that contributes to regulation, transcriptome diversity, plants.

Language: Английский

Citations

21
Principles, functions, and biological implications of m6A in plants DOI Open Access
Peizhe Song, Zhihe Cai,

Guifang Jia

et al.

RNA, Journal Year: 2024, Volume and Issue: 30(5), P. 491 - 499

Published: March 26, 2024

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

Language: Английский

Citations

7
Plant autoimmunity—fresh insights into an old phenomenon DOI Creative Commons
Matthias Freh,

Jinlan Gao,

Morten Petersen

et al.

PLANT PHYSIOLOGY, Journal Year: 2021, Volume and Issue: 188(3), P. 1419 - 1434

Published: Dec. 23, 2021

The plant immune system is well equipped to ward off the attacks of different types phytopathogens. It primarily relies on two sensors-plasma membrane-resident receptor-like kinases and intracellular nucleotide-binding domain leucine-rich repeat (NLRs) receptors that engage preferentially in pattern- effector-triggered immunity, respectively. Delicate fine-tuning, particular NLR-governed branch key prevent inappropriate deleterious activation responses. Inadequate NLR allele constellations, such as case hybrid incompatibility, mis-activation NLRs or absence modification proteins guarded by these can result spontaneous initiation defense responses cell death-a phenomenon referred autoimmunity. Here, we review recent insights augmenting our mechanistic comprehension findings broaden understanding regarding unravel candidates for likely underline necessity fine-tuning expression at various levels avoid We further present recently emerged tools study autoimmunity draw a cross-kingdom comparison role animal autoimmune conditions.

Language: Английский

Citations

33