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DNA methylation dynamics: patterns, regulation, and function DNA甲基化动力学：模式、调控和功能。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-09-18 DOI: 10.1016/j.pbi.2025.102787
Jia Gwee, Wenwen Tian, Shuiming Qian, Xuehua Zhong
{"title":"DNA methylation dynamics: patterns, regulation, and function","authors":"Jia Gwee,&nbsp;Wenwen Tian,&nbsp;Shuiming Qian,&nbsp;Xuehua Zhong","doi":"10.1016/j.pbi.2025.102787","DOIUrl":"10.1016/j.pbi.2025.102787","url":null,"abstract":"<div><div>As the crucial interface between the genome and the environment, the epigenome plays a key role in plant survival and thriving. Despite the identical DNA sequence in each nucleus of an individual, its interpretation by the cell is governed by both spatial and environmental contexts. The field of plant epigenetics is advancing rapidly with groundbreaking discoveries that are transforming our knowledge of how plants regulate gene expression, adapt to environmental changes, and uphold genomic stability. Recent technological advancements have also dramatically enhanced our ability to study the epigenome with precision, offering insights into its role at an unprecedented scale. Here, we highlight the latest findings focusing on the intricate balance of DNA methylation, the dynamic and multi-layered regulatory mechanisms, and the role and evolutionary significance of DNA methylation variations across diverse plant species. Understanding these variations in DNA methylation offers crucial insights into how plant epigenetic mechanisms regulate gene expression, genome organization, development, and responses to environmental changes.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102787"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091244","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
Complex of Proteins Associated with Set1 complexes and their increasing roles in crop improvement 与Set1复合物相关的蛋白质复合物及其在作物改良中的日益重要的作用。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-09-17 DOI: 10.1016/j.pbi.2025.102788
Jun-Yu Chen , Pan-Yi Zhang , Cheng-Guo Duan
{"title":"Complex of Proteins Associated with Set1 complexes and their increasing roles in crop improvement","authors":"Jun-Yu Chen ,&nbsp;Pan-Yi Zhang ,&nbsp;Cheng-Guo Duan","doi":"10.1016/j.pbi.2025.102788","DOIUrl":"10.1016/j.pbi.2025.102788","url":null,"abstract":"<div><div>The Complex of Proteins Associated with Set1 (COMPASS) complexes represent a group of highly conserved, multi-subunit complexes that catalyze histone H3 lysine 4 methylation across eukaryotic species. In <em>Drosophila</em> and mammals, COMPASS complexes are classified into distinct subtypes with diverse functions determined by their subunit composition. Plants have evolved analogous COMPASS assemblies that similarly exhibit functional diversification, playing pleiotropic roles in regulating vegetative growth, flowering transition, and stress adaptation. Recent studies have significantly advanced our understanding of the composition, chromatin targeting, and biological functions of plant COMPASS. In this review, we summarize the conserved core components of COMPASS in several plant species, the chromatin targeting strategies, crosstalk with other epigenetic marks, and regulatory role of COMPASS in stress adaptation. We also talk about the researches that may provide clues for crop improvement.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102788"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085290","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
Meiotic recombination and advances in quantitative trait locus mapping 减数分裂重组与数量性状位点定位研究进展。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-10-15 DOI: 10.1016/j.pbi.2025.102814
Dohwan Byun , Sang-jun Park , Kyuha Choi
{"title":"Meiotic recombination and advances in quantitative trait locus mapping","authors":"Dohwan Byun ,&nbsp;Sang-jun Park ,&nbsp;Kyuha Choi","doi":"10.1016/j.pbi.2025.102814","DOIUrl":"10.1016/j.pbi.2025.102814","url":null,"abstract":"<div><div>In plants, meiotic crossovers preferentially occur near and within genes, reshuffling preexisting genetic variation from parental genomes and thereby generating diversity in offspring. However, crossovers are generally limited to one to three per chromosome pair, tend to be widely spaced, and are rare in heterochromatic pericentromeric regions. These constraints on crossover number and distribution limit the genetic variation available for crop improvement and hinder the fine mapping of quantitative trait loci (QTLs). Unleashing meiotic crossovers has, therefore, become a key objective in plant genetics and breeding. Here, we review recent findings on pro- and anti-crossover factors that regulate crossover numbers, along with epigenetic mechanisms that suppress pericentromeric crossover recombination. We then explore genetic strategies to manipulate these regulators to maximize crossovers in both chromosomal arms and pericentromeric regions. Finally, we consider the implications of substantially elevating crossover frequency for enhancing QTL mapping resolution and accelerating plant breeding.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102814"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145307185","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
The versatile role of guard cell starch in speedy stomata: Beyond Arabidopsis 保卫细胞淀粉在快速气孔中的多功能作用：超越拟南芥
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-10-01 Epub Date: 2025-08-05 DOI: 10.1016/j.pbi.2025.102762
Hongyuan Zhang, Trang Dang, Lucia Piro, Diana Santelia
{"title":"The versatile role of guard cell starch in speedy stomata: Beyond Arabidopsis","authors":"Hongyuan Zhang,&nbsp;Trang Dang,&nbsp;Lucia Piro,&nbsp;Diana Santelia","doi":"10.1016/j.pbi.2025.102762","DOIUrl":"10.1016/j.pbi.2025.102762","url":null,"abstract":"<div><div>Engineering rapid stomatal responses to improve the coordination between stomatal conductance and carbon assimilation under fluctuating light conditions is crucial for enhancing crop productivity while conserving water. To identify promising engineering targets, we applied machine learning models to analyze published data from diverse plant lineages to reveal the primary factors driving the natural variation in the speed of stomatal opening. We highlight the versatile role of guard cell starch in integrating and modulating some of these factors and suggest starch as a previously overlooked target for optimizing stomatal function.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"87 ","pages":"Article 102762"},"PeriodicalIF":7.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144773163","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
The multifaceted roles of autophagy in plant immunity 自噬在植物免疫中的多重作用
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-10-01 Epub Date: 2025-08-30 DOI: 10.1016/j.pbi.2025.102781
Hwi Seong Jeon , Eunjeong Jang , Ohkmae K. Park
{"title":"The multifaceted roles of autophagy in plant immunity","authors":"Hwi Seong Jeon ,&nbsp;Eunjeong Jang ,&nbsp;Ohkmae K. Park","doi":"10.1016/j.pbi.2025.102781","DOIUrl":"10.1016/j.pbi.2025.102781","url":null,"abstract":"<div><div>Autophagy is a highly conserved trafficking pathway that mediates selective degradation of intracellular components via the vacuole or lysosome. Although its roles in cellular homeostasis and stress adaptation are well characterized, the specific functions of autophagy in plant immunity remain incompletely understood. Emerging evidence reveals that autophagy dynamically modulates plant immune responses, contributing to both resistance and susceptibility to a broad spectrum of pathogens. In this review, we explore recent advances in understanding the multifaceted roles of autophagy in plant immunity, with an emphasis on its mechanistic contributions to plant–microbe interactions.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"87 ","pages":"Article 102781"},"PeriodicalIF":7.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144920245","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
From genes to epidemics: Genomic insights into bacterial plant pathogen emergence. 从基因到流行病：对细菌植物病原体出现的基因组见解。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-10-01 Epub Date: 2025-08-07 DOI: 10.1016/j.pbi.2025.102765
Daniel Maddock, Michelle T Hulin
{"title":"From genes to epidemics: Genomic insights into bacterial plant pathogen emergence.","authors":"Daniel Maddock, Michelle T Hulin","doi":"10.1016/j.pbi.2025.102765","DOIUrl":"10.1016/j.pbi.2025.102765","url":null,"abstract":"<p><p>Bacterial phytopathogens are major causal agents of newly emerging plant diseases. The roles of both agricultural practices and the alteration of bacterial genomic content are well understood in the evolution of novel pathogens. However, translating this knowledge into effective tools for the comparison, prediction and understanding of current outbreaks remains challenging. To be pathogenic bacteria must be able to avoid plant immune responses, colonize host tissue and cause disease. Recent advances in both sequencing technologies and imaging techniques have provided fascinating insights into how bacterial interactions with each other and mobile genetic elements play a role in virulence evolution. This review explores these interactions, with a focus on the role of mobile genetic elements in plant pathogen evolution. Special consideration is given to how recent technologies can be applied to allow the observation of these interactions in the field and the future directions required to integrate these tools in field-based monitoring to further understand and enhance early management practices.</p>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"87 ","pages":"102765"},"PeriodicalIF":7.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803853","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
Ethylene signal integration through epigenetic mechanisms in plants 植物表观遗传机制中的乙烯信号整合
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-10-01 Epub Date: 2025-08-25 DOI: 10.1016/j.pbi.2025.102780
Aida Maric , Advait Agashe , Johanna Söntgerath , Sjon Hartman
{"title":"Ethylene signal integration through epigenetic mechanisms in plants","authors":"Aida Maric ,&nbsp;Advait Agashe ,&nbsp;Johanna Söntgerath ,&nbsp;Sjon Hartman","doi":"10.1016/j.pbi.2025.102780","DOIUrl":"10.1016/j.pbi.2025.102780","url":null,"abstract":"<div><div>Ethylene is an essential phytohormone that controls a plethora of plant developmental and stress responses. Accordingly, ethylene signal generation and progression must be under tight spatiotemporal control. This review highlights the latest milestones in understanding how epigenetic mechanisms govern ethylene biosynthesis and signaling, and how ethylene-mediated recruitment of epigenetic modifiers in turn controls gene expression and biological processes. We discuss a central mechanism of how ethylene-controlled histone acetylation is essential for ethylene signal progression. In addition, we outline how a wide range of epigenetic mechanisms control ethylene-mediated developmental and stress responses, with a focus on fruit ripening. Finally, we propose future research directions and open questions of ethylene signal integration through epigenetic mechanisms in plants.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"87 ","pages":"Article 102780"},"PeriodicalIF":7.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144893246","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
Genomic balance effects on gene expression and the organism 基因组平衡对基因表达和机体的影响
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2025-10-01 Epub Date: 2025-07-22 DOI: 10.1016/j.pbi.2025.102761
James A. Birchler, Hua Yang
{"title":"Genomic balance effects on gene expression and the organism","authors":"James A. Birchler,&nbsp;Hua Yang","doi":"10.1016/j.pbi.2025.102761","DOIUrl":"10.1016/j.pbi.2025.102761","url":null,"abstract":"<div><div>Changes in dosage of individual chromosomes have long been known to have detrimental effects on the phenotype. Molecular analyses have revealed that aneuploidy affects gene expression across the genome with the major effects being direct and inverse correlations with the varied dosage. The inverse effect is typically more prevalent especially in aneuploids with an increased chromosomal dosage. Small heterozygous deletions removing one of the two copies of a gene typically exhibit a gene dosage effect for the included genes, but larger aneuploids exhibit the global modulations. When the inverse effect also operates on the target genes being varied in an aneuploid, dosage compensation results with expression levels similar to the corresponding genomically balanced control. Most substantial aneuploids alter the total transcriptome size but with subsets of genes deviating from the general trend. The greatest reductions in transcriptome size are associated with the most detrimental phenotypic effects on the organism. Aneuploidy effects in the endosperm involve a maternal to zygotic balance or a cumulative effect typical of other tissues. Genomic balance analyses reveal the stoichiometric effects on gene regulation, the trajectory of duplicated genes in evolution, and the eventual consequences for the organism.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"87 ","pages":"Article 102761"},"PeriodicalIF":8.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144680268","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
The histone crosstalk code in plants: Deciphering epigenetic complexity 植物组蛋白串扰密码：解读表观遗传复杂性
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2025-10-01 Epub Date: 2025-07-26 DOI: 10.1016/j.pbi.2025.102763
Koki Nakamura, Nobutoshi Yamaguchi , Toshiro Ito
{"title":"The histone crosstalk code in plants: Deciphering epigenetic complexity","authors":"Koki Nakamura,&nbsp;Nobutoshi Yamaguchi ,&nbsp;Toshiro Ito","doi":"10.1016/j.pbi.2025.102763","DOIUrl":"10.1016/j.pbi.2025.102763","url":null,"abstract":"<div><div>Histone modifications are essential regulators of chromatin architecture and gene expression in plants. Traditionally, each modification was viewed as an independent signal marking specific chromatin states. However, recent advances in epigenome profiling, genome editing, and proteomics have revealed that histone marks often function in combination, engaging in hierarchical, cooperative, and antagonistic relationships. In particular, studies in <em>Arabidopsis thaliana</em> have uncovered dynamic interactions between activating and repressive modifications, as well as their coordination with DNA methylation, histone variants, and RNA modifications. Among these, H3K4 and H3K36 methylation have emerged as key regulatory hubs that integrate developmental and environmental signals into context-dependent transcriptional responses. This growing body of evidence suggests that chromatin regulation involves not isolated modifications but rather a complex network of interdependent marks. In this review, we discuss recent examples of crosstalk between histone modifications and other regulatory layers to highlight how combinatorial chromatin regulation and its underlying molecular mechanisms contribute to transcriptional control and epigenetic responsiveness in plants. Such key insights expand our understanding of the diverse and context-dependent roles of histone modifications in plant biology.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"87 ","pages":"Article 102763"},"PeriodicalIF":8.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144711006","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
Cell biology features and gene expression programs modulating cell expansion during root organ growth 根器官生长过程中调节细胞扩增的细胞生物学特性和基因表达程序
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-10-01 Epub Date: 2025-08-16 DOI: 10.1016/j.pbi.2025.102766
Camila Goldy , Virginia Barrera , Mariana Sotelo-Silveira , Ramiro E. Rodriguez
{"title":"Cell biology features and gene expression programs modulating cell expansion during root organ growth","authors":"Camila Goldy ,&nbsp;Virginia Barrera ,&nbsp;Mariana Sotelo-Silveira ,&nbsp;Ramiro E. Rodriguez","doi":"10.1016/j.pbi.2025.102766","DOIUrl":"10.1016/j.pbi.2025.102766","url":null,"abstract":"<div><div>Diffuse cell expansion mainly in the longitudinal axis of the organ significantly contributes to root organ growth. Root cell expansion is a diverse, plastic, and dynamic process, as each cell expands at specific rates and directions according to its developmental stage and in response to different ambient conditions, helping to shape the root system architecture. In this review, we focus on <em>Arabidopsis thaliana</em> to summarize the modes and magnitudes of cell expansion in both meristematic and postmitotic root cells and assess recent advances in the understanding of the transitions required for cell expansion to occur. We also elaborate on the gene expression programs that control the forces, the biochemical and the molecular mechanisms that determine cell expansion, and finally, on how variations in the magnitude and distribution of this process contribute to root adaptation to the environment.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"87 ","pages":"Article 102766"},"PeriodicalIF":7.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852670","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
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