Pub Date : 2025-10-28DOI: 10.1016/j.pbi.2025.102817
Emilia Feuerstein , Pablo Manavella , Martin Crespi , Lucia Ferrero , Federico Ariel
The functions of lncRNAs extend well beyond the traditional gene-to-protein paradigm, highlighting their ability to fine-tune gene expression without encoding proteins. Notably, lncRNAs participate in a wide range of regulatory processes, including epigenetic modifications, chromatin organization, transcriptional control, and post-transcriptional regulation. These molecules have emerged as key regulators of gene expression, playing crucial roles in modulating plant plasticity in response to environmental cues. This review discusses the current understanding of lncRNAs in shaping the three-dimensional conformation of plant chromatin, exploring their mechanisms of action and functional relevance in development and environmental responses. We also situate these findings within a broader cross-kingdom context by integrating insights from other eukaryotic systems.
{"title":"Long noncoding RNAs in plant chromatin 3D conformation dynamics","authors":"Emilia Feuerstein , Pablo Manavella , Martin Crespi , Lucia Ferrero , Federico Ariel","doi":"10.1016/j.pbi.2025.102817","DOIUrl":"10.1016/j.pbi.2025.102817","url":null,"abstract":"<div><div>The functions of lncRNAs extend well beyond the traditional gene-to-protein paradigm, highlighting their ability to fine-tune gene expression without encoding proteins. Notably, lncRNAs participate in a wide range of regulatory processes, including epigenetic modifications, chromatin organization, transcriptional control, and post-transcriptional regulation. These molecules have emerged as key regulators of gene expression, playing crucial roles in modulating plant plasticity in response to environmental cues. This review discusses the current understanding of lncRNAs in shaping the three-dimensional conformation of plant chromatin, exploring their mechanisms of action and functional relevance in development and environmental responses. We also situate these findings within a broader cross-kingdom context by integrating insights from other eukaryotic systems.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102817"},"PeriodicalIF":7.5,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145399802","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}
Pub Date : 2025-10-27DOI: 10.1016/j.pbi.2025.102818
Leandro Quadrana , Ian R. Henderson
Transposons are DNA sequences capable of self-mobilization, which occupy large fractions of plant genomes. Due to their repetitive nature, complete maps of transposon diversity have been challenging to obtain. The advent of long-read sequencing now provides high-quality pangenomic assemblies, revealing transposon diversity within and between species. Transposons are major targets of epigenetic and post-transcriptional silencing, which provide the capacity for cryptic transmission, and facilitate environmental and developmental regulation. Transposon distributions are highly structured along plant chromosomes and we examine genomic niches that specific families are adapted to occupy. Here, we review new insights into transposon core and accessory proteins, and how these can regulate activity in vivo. Finally, we consider the role of transposons in host genome adaptation and evolution, as well as how they are selected on their own terms.
{"title":"The natural history of transposons in plant pangenomes and panepigenomes","authors":"Leandro Quadrana , Ian R. Henderson","doi":"10.1016/j.pbi.2025.102818","DOIUrl":"10.1016/j.pbi.2025.102818","url":null,"abstract":"<div><div>Transposons are DNA sequences capable of self-mobilization, which occupy large fractions of plant genomes. Due to their repetitive nature, complete maps of transposon diversity have been challenging to obtain. The advent of long-read sequencing now provides high-quality pangenomic assemblies, revealing transposon diversity within and between species. Transposons are major targets of epigenetic and post-transcriptional silencing, which provide the capacity for cryptic transmission, and facilitate environmental and developmental regulation. Transposon distributions are highly structured along plant chromosomes and we examine genomic niches that specific families are adapted to occupy. Here, we review new insights into transposon core and accessory proteins, and how these can regulate activity <em>in vivo</em>. Finally, we consider the role of transposons in host genome adaptation and evolution, as well as how they are selected on their own terms.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102818"},"PeriodicalIF":7.5,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145387679","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}
Pub Date : 2025-10-24DOI: 10.1016/j.pbi.2025.102816
Deepak D. Bhandari , Sang-Jin Kim , Federica Brandizzi
The plant cell wall (CW) was long thought to be a rigid barrier encasing the plant cell and protecting it against biotic and abiotic stressors. Different CW polysaccharides interact with each other, and modifications of either the components or organization of these polysaccharides result in impaired growth or immunity. Emerging evidence suggests that the CW is dynamically modified and reorganized based on internal and external cues. Thus, the CW is both the first barrier that pathogens encounter and the critical final step in defense signaling that leads to fortification of the CW. Here, we review recent findings on how CW components are remodeled to fortify the CW upon pathogen attack and propose a novel concept: layered CW remodeling as an immune strategy. Within this framework, we categorize three interconnected layers of CW remodeling upon pathogen attack: (i) rapid and reversible CW depositions that provide immediate but transient protection; (ii) flexible modifications with plausible signaling functions that integrate defense and surveillance; and (iii) irreversible fortifications that encase pathogen, delimiting infected cells from uninfected cells. This layered framework provides a cohesive view of how different CW modifications are integrated into, and contribute to, plant defense. We also discuss the challenges in studying CW modifications during biotic stresses and highlight important questions that remain unanswered.
{"title":"Fortifying the frontier: cell wall modifications during plant immunity","authors":"Deepak D. Bhandari , Sang-Jin Kim , Federica Brandizzi","doi":"10.1016/j.pbi.2025.102816","DOIUrl":"10.1016/j.pbi.2025.102816","url":null,"abstract":"<div><div>The plant cell wall (CW) was long thought to be a rigid barrier encasing the plant cell and protecting it against biotic and abiotic stressors. Different CW polysaccharides interact with each other, and modifications of either the components or organization of these polysaccharides result in impaired growth or immunity. Emerging evidence suggests that the CW is dynamically modified and reorganized based on internal and external cues. Thus, the CW is both the first barrier that pathogens encounter and the critical final step in defense signaling that leads to fortification of the CW. Here, we review recent findings on how CW components are remodeled to fortify the CW upon pathogen attack and propose a novel concept: layered CW remodeling as an immune strategy. Within this framework, we categorize three interconnected layers of CW remodeling upon pathogen attack: (i) rapid and reversible CW depositions that provide immediate but transient protection; (ii) flexible modifications with plausible signaling functions that integrate defense and surveillance; and (iii) irreversible fortifications that encase pathogen, delimiting infected cells from uninfected cells. This layered framework provides a cohesive view of how different CW modifications are integrated into, and contribute to, plant defense. We also discuss the challenges in studying CW modifications during biotic stresses and highlight important questions that remain unanswered.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102816"},"PeriodicalIF":7.5,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358129","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}
Pub Date : 2025-10-18DOI: 10.1016/j.pbi.2025.102813
Patricia León , Julio Sierra , Ryan P. McQuinn
Plastids are multifunctional plant organelles, acting as crucial environmental sensors and metabolic hubs that influence plant development and responses to environmental cues. This integration depends on bidirectional communication between plastids and the nucleus. While anterograde regulation is extensively characterized, biogenic retrograde signaling arising during plastid differentiation, remains incompletely understood. Traditionally focused on chloroplasts, studies have identified tetrapyrroles such as heme as key signals. However, recent findings support carotenoid-derived apocarotenoids, particularly those from acyclic cis-carotenes, as emerging retrograde signals. These signals function not only under stress but also during normal chloroplast developmental transitions, such as de-etiolation, and can act as either positive or negative regulators depending on the context. Evidence from grasses suggests that chloroplast differentiation proceeds through sequential, stage-specific signals serving as developmental checkpoints. Moreover, biogenic signaling tunes nuclear gene expression through transcription factors, chromatin remodeling and posttranslational regulation. This review synthesizes current knowledge on biogenic retrograde signaling, highlighting its role in plastid differentiation, development and adaptation. We emphasize the emerging roles of apocarotenoids, highly sensitive to metabolic and environmental conditions, as potential retrograde signals. We highlight that broader studies on different plastid types, novel metabolites and regulatory networks are essential to unravel the complexity of plastid-to-nucleus communication and its key roles in plant morphogenesis and adaptation to environmental changes.
{"title":"Deciphering plastid retrograde signals and their roles in plant development","authors":"Patricia León , Julio Sierra , Ryan P. McQuinn","doi":"10.1016/j.pbi.2025.102813","DOIUrl":"10.1016/j.pbi.2025.102813","url":null,"abstract":"<div><div>Plastids are multifunctional plant organelles, acting as crucial environmental sensors and metabolic hubs that influence plant development and responses to environmental cues. This integration depends on bidirectional communication between plastids and the nucleus. While anterograde regulation is extensively characterized, biogenic retrograde signaling arising during plastid differentiation, remains incompletely understood. Traditionally focused on chloroplasts, studies have identified tetrapyrroles such as heme as key signals. However, recent findings support carotenoid-derived apocarotenoids, particularly those from acyclic <em>cis</em>-carotenes, as emerging retrograde signals. These signals function not only under stress but also during normal chloroplast developmental transitions, such as de-etiolation, and can act as either positive or negative regulators depending on the context. Evidence from grasses suggests that chloroplast differentiation proceeds through sequential, stage-specific signals serving as developmental checkpoints. Moreover, biogenic signaling tunes nuclear gene expression through transcription factors, chromatin remodeling and posttranslational regulation. This review synthesizes current knowledge on biogenic retrograde signaling, highlighting its role in plastid differentiation, development and adaptation. We emphasize the emerging roles of apocarotenoids, highly sensitive to metabolic and environmental conditions, as potential retrograde signals. We highlight that broader studies on different plastid types, novel metabolites and regulatory networks are essential to unravel the complexity of plastid-to-nucleus communication and its key roles in plant morphogenesis and adaptation to environmental changes.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102813"},"PeriodicalIF":7.5,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145328226","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}
Pub Date : 2025-10-17DOI: 10.1016/j.pbi.2025.102815
Xin Xu , Xin-Jian He
Histone acetyltransferase (HAT) complexes are pivotal regulators of chromatin dynamics, orchestrating transcriptional programs essential for plant development and stress responses in plants. This review synthesizes recent advances in the classification, subunit composition, and functional mechanisms of plant HAT complexes, emphasizing plant-specific characteristics compared to the conserved architecture of HAT complexes. By integrating genetic, biochemical, and structural studies, we delineate how these complexes modulate histone acetylation and coordinate with other chromatin modifications to regulate gene expression. Further research should focus on deciphering the spatiotemporal regulation of HAT complex composition and histone acetylation, and determining the targeting mechanisms of these complexes.
{"title":"Plant histone acetyltransferase complexes: Conserved and plant-specific characteristics","authors":"Xin Xu , Xin-Jian He","doi":"10.1016/j.pbi.2025.102815","DOIUrl":"10.1016/j.pbi.2025.102815","url":null,"abstract":"<div><div>Histone acetyltransferase (HAT) complexes are pivotal regulators of chromatin dynamics, orchestrating transcriptional programs essential for plant development and stress responses in plants. This review synthesizes recent advances in the classification, subunit composition, and functional mechanisms of plant HAT complexes, emphasizing plant-specific characteristics compared to the conserved architecture of HAT complexes. By integrating genetic, biochemical, and structural studies, we delineate how these complexes modulate histone acetylation and coordinate with other chromatin modifications to regulate gene expression. Further research should focus on deciphering the spatiotemporal regulation of HAT complex composition and histone acetylation, and determining the targeting mechanisms of these complexes.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102815"},"PeriodicalIF":7.5,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318251","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}
Pub Date : 2025-10-15DOI: 10.1016/j.pbi.2025.102812
Hee-Kyung Ahn , Jonathan D.G. Jones , Guanghao Guo
Effector-triggered immunity (ETI) can be defined as immune responses activated upon specific recognition of a pathogen effector protein by its cognate plant immune receptor protein. This classic gene-for-gene model of the interaction of one pathogen effector, also known as an Avirulence (Avr) gene, with one plant immune receptor gene, known as a Resistance (R) gene has been documented since the 1950s. Since then, different types of recognition that deviate from the gene-for-gene model, for example, immune receptor pairs and immune receptor networks, have been identified. In addition, while many R genes encode NLR (nucleotide binding, leucine rich repeat) proteins, R genes that encode only parts of NLR domains, and non-NLR encoding R genes such as tandem kinases have been identified, broadening the immune receptor repertoire in plants. In recent years, there have been significant advances in understanding the molecular mechanisms of NLR intracellular immune receptors in plants, including how they are inhibited, activated, and regulated. This review covers recent developments in ETI initiation mechanisms and in plant NLR biology.
{"title":"Variations on a theme: Non-canonical mechanisms of effector-triggered immunity","authors":"Hee-Kyung Ahn , Jonathan D.G. Jones , Guanghao Guo","doi":"10.1016/j.pbi.2025.102812","DOIUrl":"10.1016/j.pbi.2025.102812","url":null,"abstract":"<div><div>Effector-triggered immunity (ETI) can be defined as immune responses activated upon specific recognition of a pathogen effector protein by its cognate plant immune receptor protein. This classic gene-for-gene model of the interaction of one pathogen effector, also known as an <em>Avirulence</em> (<em>Avr</em>) gene, with one plant immune receptor gene, known as a <em>Resistance</em> (<em>R</em>) gene has been documented since the 1950s. Since then, different types of recognition that deviate from the gene-for-gene model, for example, immune receptor pairs and immune receptor networks, have been identified. In addition, while many <em>R</em> genes encode NLR (nucleotide binding, leucine rich repeat) proteins, <em>R</em> genes that encode only parts of NLR domains, and non-NLR encoding <em>R</em> genes such as tandem kinases have been identified, broadening the immune receptor repertoire in plants. In recent years, there have been significant advances in understanding the molecular mechanisms of NLR intracellular immune receptors in plants, including how they are inhibited, activated, and regulated. This review covers recent developments in ETI initiation mechanisms and in plant NLR biology.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102812"},"PeriodicalIF":7.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145307187","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}
Pub Date : 2025-10-15DOI: 10.1016/j.pbi.2025.102814
Dohwan Byun , Sang-jun Park , Kyuha Choi
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.
{"title":"Meiotic recombination and advances in quantitative trait locus mapping","authors":"Dohwan Byun , Sang-jun Park , 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":"2025-10-15","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}
Pub Date : 2025-10-10DOI: 10.1016/j.pbi.2025.102808
Lea Sophie Berg , Michael Thomas Raissig
Grass stomata provide an exemplary model of how form can improve functionality and promote the success of a plant family. The four-celled grass stomata are composed of dumbbell-shaped guard cells, each flanked by a single parallel subsidiary cell–arguably the most derived and fastest stomatal morphotype. The grasses' breathing pores develop in a strictly linear gradient within a stereotypically patterned epidermis, making it a highly accessible and spatiotemporally predictable developmental study system. Here, we highlight our current understanding of how vein-associated establishment of stomatal identity, tightly regulated asymmetric and symmetric cell division programs and extraordinary morphogenetic processes orchestrate the development of these uniquely shaped graminoid stomata. The innovative geometry and cellular composition of grass stomata have been repeatedly linked to rapid stomatal opening and closing kinetics, thus contributing to the grasses’ water-use-efficient photosynthesis. Therefore, besides revealing fundamental aspects of plant development and plant cell biology, the dissection of the developmental processes forming grass stomata can also highlight strategies to engineer stomatal morphology for improved plant-atmosphere gas exchange.
{"title":"Stomatal patterning and development in grasses","authors":"Lea Sophie Berg , Michael Thomas Raissig","doi":"10.1016/j.pbi.2025.102808","DOIUrl":"10.1016/j.pbi.2025.102808","url":null,"abstract":"<div><div>Grass stomata provide an exemplary model of how form can improve functionality and promote the success of a plant family. The four-celled grass stomata are composed of dumbbell-shaped guard cells, each flanked by a single parallel subsidiary cell–arguably the most derived and fastest stomatal morphotype. The grasses' breathing pores develop in a strictly linear gradient within a stereotypically patterned epidermis, making it a highly accessible and spatiotemporally predictable developmental study system. Here, we highlight our current understanding of how vein-associated establishment of stomatal identity, tightly regulated asymmetric and symmetric cell division programs and extraordinary morphogenetic processes orchestrate the development of these uniquely shaped graminoid stomata. The innovative geometry and cellular composition of grass stomata have been repeatedly linked to rapid stomatal opening and closing kinetics, thus contributing to the grasses’ water-use-efficient photosynthesis. Therefore, besides revealing fundamental aspects of plant development and plant cell biology, the dissection of the developmental processes forming grass stomata can also highlight strategies to engineer stomatal morphology for improved plant-atmosphere gas exchange.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102808"},"PeriodicalIF":7.5,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145262908","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}
Pub Date : 2025-10-09DOI: 10.1016/j.pbi.2025.102810
Jason Gardiner
In plants, altering the accessibility to DNA through chromatin modification is a key component of transcriptome regulation, crucial for normal development and environmental response. In recent years, our understanding of how and why plants engineer their chromatin has greatly improved, leading to strategies that now enable us to engineer chromatin through both targeted and non-targeted approaches. Although new and improved systems for chromatin engineering are continually emerging, it is evident that developing a diverse toolbox of strategies to tackle various unique challenges is necessary. This review outlines different methods for non-targeted and targeted chromatin engineering, enabling the manipulation of the transcriptome through chromatin engineering. It also discusses particular challenges in the field of chromatin engineering in plants and offers a brief outlook on potential future directions.
{"title":"Engineering chromatin and transcriptome regulation in plants: Strategies, challenges, and outlook","authors":"Jason Gardiner","doi":"10.1016/j.pbi.2025.102810","DOIUrl":"10.1016/j.pbi.2025.102810","url":null,"abstract":"<div><div>In plants, altering the accessibility to DNA through chromatin modification is a key component of transcriptome regulation, crucial for normal development and environmental response. In recent years, our understanding of how and why plants engineer their chromatin has greatly improved, leading to strategies that now enable us to engineer chromatin through both targeted and non-targeted approaches. Although new and improved systems for chromatin engineering are continually emerging, it is evident that developing a diverse toolbox of strategies to tackle various unique challenges is necessary. This review outlines different methods for non-targeted and targeted chromatin engineering, enabling the manipulation of the transcriptome through chromatin engineering. It also discusses particular challenges in the field of chromatin engineering in plants and offers a brief outlook on potential future directions.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102810"},"PeriodicalIF":7.5,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145262907","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}
Pub Date : 2025-10-08DOI: 10.1016/j.pbi.2025.102809
Cassandra Maranas, Jennifer L. Nemhauser
Across all biological life, cells in the same environment, with exposure to the same signals and cues exhibit differences in gene expression patterns. This phenomenon is deemed noise and it has long been a question whether it serves a functional role. In plants, recent advances indicate that noise enables many cell fate decisions and thus triggers organogenesis. Additionally, evidence suggests that noise allows organisms to adapt to dynamic environmental conditions and stressors. Given these recent findings and the increasing pressures of climate change on agriculture, efforts to understand the sources and effects of noise are crucial for future projects in engineering resilient, adaptable crops. In this review, we discuss how plants manage noisy gene expression, in some cases buffering and in some cases amplifying natural transcriptional noise. We also discuss the downstream implications of cell to cell heterogeneity on developmental outcomes and robustness. We describe recent progress in this area and present the possibility of using gene expression variability as an engineering target.
{"title":"Building resilience by cultivating difference: A role for noise in development","authors":"Cassandra Maranas, Jennifer L. Nemhauser","doi":"10.1016/j.pbi.2025.102809","DOIUrl":"10.1016/j.pbi.2025.102809","url":null,"abstract":"<div><div>Across all biological life, cells in the same environment, with exposure to the same signals and cues exhibit differences in gene expression patterns. This phenomenon is deemed noise and it has long been a question whether it serves a functional role. In plants, recent advances indicate that noise enables many cell fate decisions and thus triggers organogenesis. Additionally, evidence suggests that noise allows organisms to adapt to dynamic environmental conditions and stressors. Given these recent findings and the increasing pressures of climate change on agriculture, efforts to understand the sources and effects of noise are crucial for future projects in engineering resilient, adaptable crops. In this review, we discuss how plants manage noisy gene expression, in some cases buffering and in some cases amplifying natural transcriptional noise. We also discuss the downstream implications of cell to cell heterogeneity on developmental outcomes and robustness. We describe recent progress in this area and present the possibility of using gene expression variability as an engineering target.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102809"},"PeriodicalIF":7.5,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257589","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}
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