Journal of Experimental Botany最新文献

Plant epigenetics: controlling genome expression to integrate developmental and environmental cues. 植物表观遗传学：控制基因组表达以整合发育和环境线索。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/eraf134

Marco Catoni, Tamara Lechon Gomez, Aline V Probst

引用次数: 0

Partial redundancy buffers deleterious effects of mutating DNA methyltransferase 1-1 (MET1-1) in polyploid wheat. 部分冗余缓冲了多倍体小麦DNA甲基转移酶1-1 （MET1-1）突变的有害影响。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/eraf016

Samuel Burrows, Delfi Dorussen, Joseph Crudgington, Giorgia Di Santolo, James Simmonds, Marco Catoni, Philippa Borrill

{"title":"Partial redundancy buffers deleterious effects of mutating DNA methyltransferase 1-1 (MET1-1) in polyploid wheat.","authors":"Samuel Burrows, Delfi Dorussen, Joseph Crudgington, Giorgia Di Santolo, James Simmonds, Marco Catoni, Philippa Borrill","doi":"10.1093/jxb/eraf016","DOIUrl":"10.1093/jxb/eraf016","url":null,"abstract":"DNA methylation plays important roles in gene expression, transposable element silencing, and genome stability. Altering DNA methylation could generate additional phenotypic variation for crop breeding, however the lethality of epigenetic mutants in crop species has hindered its investigation. Here, we exploit partial redundancy between homoeologues in polyploid wheat to generate viable mutants in the DNA methyltransferase 1-1 (MET1-1) gene with altered methylation profiles. In Triticum turgidum (tetraploid wheat) and Triticum aestivum (hexaploid wheat), we found under-representation of higher order mutants (5/6 and 6/6 mutant met1-1 copies in hexaploid wheat and 3/4 and 4/4 copies in tetraploid wheat) when genotyping segregating seeds and seedlings, due to reduced transmission of null mutant gametes from the paternal and maternal side. The loss of four or more functional copies of MET1-1 results in decreased CG methylation in hexaploid wheat. Changes to gene expression increase stepwise with the number of mutant alleles, suggesting a dosage-dependent effect. We identified heritable changes to flowering and awn phenotypes which segregate independently of MET1-1. Together our results demonstrate that polyploidy can be leveraged to generate quantitative changes to CG methylation without the lethal consequences observed in other crops.","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2500-2516"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Using targeted genome methylation for crop improvement. 利用靶向基因组甲基化进行作物改良。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/eraf131

Zhibo Wang, Rebecca S Bart

{"title":"Using targeted genome methylation for crop improvement.","authors":"Zhibo Wang, Rebecca S Bart","doi":"10.1093/jxb/eraf131","DOIUrl":"10.1093/jxb/eraf131","url":null,"abstract":"Genome editing allows scientists to specifically change the DNA sequence of an organism. This powerful technology now fuels basic biology discovery and tangible crop improvement efforts. There is a less well understood layer of information encoded in genomes, known collectively as 'epigenetics', that impacts gene expression, without changing the DNA sequence. Epigenetic processes allow organisms to rapidly respond to environmental fluctuation. Like genome editing, recent advances have demonstrated that it is possible to edit the epigenome of a plant and cause heritable phenotypic changes. In this review, we aim to specifically consider the unique advantages that targeted epigenome editing might provide over existing biotechnology tools. This review is aimed at a broad audience. We begin with a high-level overview of the tools currently available for crop improvement. Next, we present a more detailed overview of the key discoveries that have been made in recent years, primarily using the model system Arabidopsis, new efforts to extend targeted methylation to crop plants, the current status of the technology, and the challenges that remain to realize the full potential of targeted epigenome editing. We end with a forward-looking commentary on how epi-alleles might interface with breeding programs across a variety of crops.","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2394-2404"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cytidine analogs in plant epigenetic research and beyond. 胞苷类似物在植物表观遗传学研究中的应用。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/erae522

Eva Dvořák Tomaštíková, Ales Pecinka

{"title":"Cytidine analogs in plant epigenetic research and beyond.","authors":"Eva Dvořák Tomaštíková, Ales Pecinka","doi":"10.1093/jxb/erae522","DOIUrl":"10.1093/jxb/erae522","url":null,"abstract":"Cytosine (DNA) methylation plays important roles in silencing transposable elements, plant development, genomic imprinting, stress responses, and maintenance of genome stability. To better understand the functions of this epigenetic modification, several tools have been developed to manipulate DNA methylation levels. These tools include mutants of DNA methylation writers and readers, targeted manipulation of locus-specific methylation, and the use of chemical inhibitors. Here, we summarize the effects of commonly used cytidine analog chemical inhibitors, represented by zebularine, 5-azacytidine, and their related compounds, on plants. These analogs are incorporated into chromosomal DNA, where they block the activity of the replicative CG DNA methyltransferase 1 (MET1). This leads to manifold alterations in the plant epigenome, modified developmental programs, or suppression of hybridization barriers. We also highlight the DNA-damaging effects of cytidine analogs, particularly the formation of stable DNA-protein crosslinks between DNA and MET1. This phenomenon sheds new light on specific phenotypes observed upon treatment with cytidine analogs. In conclusion, cytidine analogs are a vital tool for plant genome research and have the potential to open new promising avenues for applications in plant biotechnology and breeding.","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2419-2432"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Non-coding and epigenetic mechanisms in the regulation of seed germination in Arabidopsis thaliana. 拟南芥种子萌发调控的非编码和表观遗传机制。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/eraf051

Benjamin J M Tremblay, Julia I Qüesta

引用次数: 0

TORquing chromatin: the regulatory role of TOR kinase in chromatin function. TORquing chromatin：TOR 激酶对染色质功能的调控作用。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/erae474

Yihan Dong, Fatemeh Aflaki, Iva Mozgova, Alexandre Berr

引用次数: 0

The H3K27me3 histone mark correlates with repression of colour and aroma development post-harvest in strawberry fruit. H3K27me3 组蛋白标记与草莓果实采后色泽和香气发育的抑制相关。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/erae464

Ashley Baldwin, Tamara Lechon, Angela Marchbank, Simon Scofield, Kerstin Lieu, Charlotte L Wilson, Richard A Ludlow, Robert J Herbert, Hans-Wilhelm Nützmann, Hilary J Rogers

{"title":"The H3K27me3 histone mark correlates with repression of colour and aroma development post-harvest in strawberry fruit.","authors":"Ashley Baldwin, Tamara Lechon, Angela Marchbank, Simon Scofield, Kerstin Lieu, Charlotte L Wilson, Richard A Ludlow, Robert J Herbert, Hans-Wilhelm Nützmann, Hilary J Rogers","doi":"10.1093/jxb/erae464","DOIUrl":"10.1093/jxb/erae464","url":null,"abstract":"Strawberry ripening is non-climacteric, and post-harvest fruit enter senescence and deteriorate rapidly. Chilled storage induces transcriptome-wide changes in gene expression, including down-regulation of aroma-related genes. Histone marks are associated with transcriptional activation or repression; the H3K27me3 mark is mainly associated with repression of gene expression. Here genes associated with H3K27me3 were identified through ChIP-seq in ripe red strawberry fruit at harvest and after 5 d of chilled storage in the dark. The number of ChIP peaks increased with storage time, indicating an increased role for this mark in regulation of gene expression following chilled dark storage. Comparing ChIP-seq data with RNA-seq data from the same material identified 440 genes whose expression correlated with H3K27me3 repression. Abiotic stress genes, especially cold stress response genes, were down-regulated during storage. Increased association with the H3K27me3 mark indicated that they may be repressed via this epigenetic mark. Other functional groups included cell wall and carbohydrate metabolism. The association with the H3K27me3 mark of two transcription factor genes (FaHY5 and FaTRAB1) and of FaADH, involved in ester biosynthesis, was validated by ChIP-PCR. These three genes were all down-regulated during storage and indicated a network of H3K27me3 gene repression affecting both anthocyanin and ester biosynthesis.","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2487-2499"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A complex interplay between histone variants and DNA methylation. 组蛋白变异和DNA甲基化之间的复杂相互作用。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/eraf030

Alejandro Edera, Leandro Quadrana

引用次数: 0

Non-CG DNA methylation represses SDC expression to modulate hypocotyl elongation during thermormorphogenesis in Arabidopsis. 在热形态形成过程中，非cg DNA甲基化抑制SDC表达以调节下胚轴伸长。

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/eraf105

Maián Garro, Eleonora Greco, Gustavo J Vannay, Aleksandra Leonova, Leonardo Bruno, Matías Capella

{"title":"Non-CG DNA methylation represses SDC expression to modulate hypocotyl elongation during thermormorphogenesis in Arabidopsis.","authors":"Maián Garro, Eleonora Greco, Gustavo J Vannay, Aleksandra Leonova, Leonardo Bruno, Matías Capella","doi":"10.1093/jxb/eraf105","DOIUrl":"10.1093/jxb/eraf105","url":null,"abstract":"Plants adapt to warm environments through physiological and morphological changes termed thermomorphogenesis, which involve transcriptional reprogramming exerted mainly by PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Fluctuating temperatures can also influence the patterns of cytosine DNA methylation (DNAme), thereby influencing gene expression; however, whether these epigenetic changes provide an adaptative advantage remains unclear. Here, we provide evidence that DNAme is required to regulate thermomorphogenesis in Arabidopsis. Hypomethylated drm1 drm2 cmt3 mutants and seedlings treated with 5-azacytidine to block DNAme exhibited reduced hypocotyl growth at warm temperatures, primarily due to impaired cell elongation. Moreover, DNA hypomethylation compromised auxin biosynthesis and transport in response to warmth, partially by reducing PIF4 protein levels. Notably, the loss of DNAme led to increased expression of SUPPRESSOR OF drm1 drm2 cmt3 (SDC), which in turn restricted hypocotyl elongation during thermomorphogenesis. Finally, DNAme was found to regulate the inhibition of SDC expression to promote gibberellin biosynthesis. Our findings underscore the critical role of DNAme in modulating gene expression in response to temperature fluctuations and provide new insights into the epigenetic regulation of thermomorphogenesis.","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2517-2534"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA methylation dynamics in the shoot apical meristem. 嫩枝顶端分生组织中 DNA 甲基化的动态变化

IF 5.6 2区生物学

Journal of Experimental Botany Pub Date : 2025-06-17 DOI: 10.1093/jxb/eraf024

Jie Yang, Frank Johannes

引用次数: 0