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Fine-scale 3D chromatin architectures and their regulatory mechanisms in plants 植物精细三维染色质结构及其调控机制
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-09-15 DOI: 10.1016/j.pbi.2025.102786
Suxin Xiao, Lingxiao Luo, Minqi Yang, Hang He, Yue Zhou
Recent studies have demonstrated that fine-scale chromatin architectures, including topologically associating domains (TADs) and chromatin loops, play critical roles in plant growth and development. Advanced technologies with increased resolution and reduced sequencing costs have provided more detailed interaction information, enabling the identification of additional chromatin loops and their associated biological processes. In this review, we present a comprehensive overview of the technologies that have been successfully applied in plants, followed by a detailed description of KNOT, fountain, TAD and chromatin loop. At the same time, some regulators associated with three-dimensional (3D) chromatin architectures are also discussed to understand the regulation of 3D chromatin architecture in plants. Furthermore, this review offers directions of 3D chromatin architecture in plants in terms of both technological developments and scientific mechanisms.
最近的研究表明,精细尺度的染色质结构,包括拓扑相关结构域(TADs)和染色质环,在植物的生长发育中起着至关重要的作用。具有更高分辨率和更低测序成本的先进技术提供了更详细的相互作用信息,使鉴定额外的染色质环及其相关的生物学过程成为可能。本文综述了目前已成功应用于植物的相关技术,并对KNOT、fountain、TAD和chromatin loop进行了详细的介绍。同时,还讨论了一些与三维染色质结构相关的调控因子,以了解植物三维染色质结构的调控。此外,本文还对植物三维染色质结构的技术发展和科学机制等方面进行了综述。
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引用次数: 0
The cellular epigenetic blueprint of plant regeneration 植物再生的细胞表观遗传蓝图
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-09-03 DOI: 10.1016/j.pbi.2025.102784
Yiting He , Lin Xu , Qikun Liu
Plants exhibit remarkable regenerative capacities, enabling tissue repair, de novo organogenesis, and somatic embryogenesis in response to mechanical injury or phytohormone induction. At the cellular level, this process is driven by the establishment of pluripotency and cell fate specification, regulated through dynamic epigenomic remodeling. Emerging studies have begun to unravel the intricate regulatory circuits governing regeneration in a cell-type- and lineage-specific manner. In this short review, we synthesize key findings from interconnected studies, exploring potential common mechanisms underlying the epigenetic regulation of plant regeneration. We also highlight promising research directions, emerging tools, and innovative strategies to investigate plant regeneration epigenetics at single-cell and single-cell-type resolution. These technological advances will provide critical insights into plant cell fate determination, the fundamental process governing regeneration.
植物表现出显著的再生能力,能够在机械损伤或植物激素诱导下进行组织修复、新生器官发生和体细胞胚胎发生。在细胞水平上,这一过程是由多能性和细胞命运规范的建立驱动的,通过动态表观基因组重塑来调节。新兴的研究已经开始揭示以细胞类型和谱系特异性方式控制再生的复杂调控电路。在这篇简短的综述中,我们综合了相关研究的关键发现,探索了植物再生表观遗传调控的潜在共同机制。我们还重点介绍了在单细胞和单细胞类型分辨率下研究植物再生表观遗传学的前景研究方向、新兴工具和创新策略。这些技术进步将为植物细胞命运的决定提供重要的见解,这是控制再生的基本过程。
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引用次数: 0
Position and identity, two separable but inseparable processes in floral meristem patterning 位置和身份,花分生组织形成过程中两个可分离但不可分割的过程
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-09-01 DOI: 10.1016/j.pbi.2025.102785
Ya Min
Early floral meristem (FM) patterning is one of the most intensively studied developmental programs in plants. While extensive work has uncovered the molecular networks underlying key processes such as organ initiation and identity specification, integrating this knowledge into a comprehensive framework remains challenging. Organ initiation is governed by auxin-mediated positioning and boundary formation, whereas organ identity is determined by the combinatorial activities of ABCE-class transcription factors. These processes have often been studied in isolation, even though proper flower development requires their coordination in space and time. This review synthesizes current insights into early floral organ initiation and identity determination, and potential molecular links bridging these two programs. I also discuss persistent gaps in our understanding, the challenges in addressing these knowledge gaps, and how emerging tools can help disentangle the complex crosstalk between initiation and identity, ultimately advancing a more integrated view of the regulatory networks that pattern the early FM.
早期花分生组织(FM)的形成是植物发育过程中研究最深入的过程之一。虽然大量的工作已经揭示了诸如器官起始和身份规范等关键过程的分子网络,但将这些知识整合到一个全面的框架中仍然具有挑战性。器官起始是由生长素介导的定位和边界形成决定的,而器官身份是由abce类转录因子的组合活性决定的。这些过程经常被孤立地研究,尽管适当的花发育需要它们在空间和时间上的协调。本文综述了目前对早期花器官形成和身份决定的研究进展,以及连接这两个过程的潜在分子联系。我还讨论了我们理解中持续存在的差距,解决这些知识差距的挑战,以及新兴工具如何帮助解开起始和身份之间复杂的串扰,最终推进对早期FM模式的监管网络的更综合的看法。
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引用次数: 0
Interplay between Polycomb-group associated histone modifiers and accessory proteins in plant evolution Polycomb-group相关组蛋白修饰因子与辅助蛋白在植物进化中的相互作用
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-09-01 DOI: 10.1016/j.pbi.2025.102783
Ahamed Khan, Biswajit Ghosh, Daniel Schubert
Epigenetic regulators are multiprotein complexes that modify chromatin architecture to control gene expression in response to developmental and environmental cues. These complexes function in a highly coordinated manner, often collaborating with various accessory proteins to precisely regulate the dynamic nature of chromatin states. However, our understanding of how these core histone-modifying regulators co-evolved with accessory proteins during plant evolution remains limited. Therefore, in this review, we summarize the evolution of major histone modification regulators, with a focus on Polycomb group complexes and their associated accessory proteins. We discuss how accessory proteins have evolved to modulate the activity of conserved core components, supporting key innovations during plant evolution. Lastly, we highlight the role of accessory proteins in mediating crosstalk between histone-modifying complexes, emerging as key evolutionary factors that shape the epigenetic landscape and influence plant development and environmental adaptation.
表观遗传调控因子是一种多蛋白复合物,它通过改变染色质结构来控制基因表达,以响应发育和环境的提示。这些复合物以高度协调的方式发挥作用,经常与各种辅助蛋白合作,精确调节染色质状态的动态性质。然而,我们对这些核心组蛋白修饰调节因子在植物进化过程中如何与辅助蛋白共同进化的理解仍然有限。因此,在这篇综述中,我们总结了主要的组蛋白修饰调节因子的进化,重点介绍了Polycomb基团复合物及其相关的辅助蛋白。我们讨论了辅助蛋白如何进化以调节保守核心成分的活性,支持植物进化过程中的关键创新。最后,我们强调了辅助蛋白在调节组蛋白修饰复合物之间的串扰中的作用,作为塑造表观遗传景观和影响植物发育和环境适应的关键进化因素。
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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 Q1 PLANT SCIENCES Pub Date : 2025-08-30 DOI: 10.1016/j.pbi.2025.102781
Hwi Seong Jeon , Eunjeong Jang , Ohkmae K. Park
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.
自噬是一种高度保守的运输途径,通过液泡或溶酶体介导细胞内成分的选择性降解。虽然自噬在细胞稳态和逆境适应中的作用已经被很好地描述,但自噬在植物免疫中的具体功能仍然不完全清楚。新出现的证据表明,自噬动态调节植物的免疫反应,有助于对广泛的病原体的抗性和易感性。在这篇综述中,我们探讨了自噬在植物免疫中的多方面作用的最新进展,重点介绍了自噬在植物与微生物相互作用中的机制贡献。
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引用次数: 0
Sense and sensitivity - decoding calcium signalling across cellular, autocrine, paracrine and endocrine pathways in plant resilience 感觉和敏感性-解码钙信号通过细胞,自分泌,旁分泌和内分泌途径在植物恢复力
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-08-30 DOI: 10.1016/j.pbi.2025.102782
Sarah Lederer , Anja Liese , Justin Lee , Tina Romeis
Calcium (Ca2+) signalling plays a central role in plant immunity, as underscored by recent findings showing that many disease resistance mechanisms result in formation of Ca2+-permeable pores, and that optogenetic activation of Ca2+ influx is sufficient to trigger immune responses. This review emphasizes on Ca2+ decoding, i.e. how diverse intracellular proteins interpret Ca2+ signals to drive cellular reactions. States of “Ca2+ responsiveness” — defined by the distinct sensitivities of various decoders and additional sensitization mechanisms — contribute to the regulation of immunity, possibly including the mutual potentiation of pattern- and effector-triggered immunity pathways. Additionally, the “PRIMER-bystander” model of immune signalling is interpreted within this decoding framework. Here, infected cells are proposed to enter a primed (PRIMER) immune state through strong Ca2+ signals derived from resistosome pores, while adjacent bystander cells respond to spreading signalling molecules from their neighbours. Through this spatial arrangement, coordination is achieved between cell-autonomous (autocrine) responses and non-autonomous (paracrine or endocrine) signalling, allowing robust immune propagation across plant tissues. By framing plant immunity through this Ca2+ “sense and sensitivity” paradigm, insights are provided into immune system robustness, and potential targets may be identified for future development of disease-resistant, climate-resilient crops.
钙(Ca2+)信号在植物免疫中起着核心作用,最近的研究结果表明,许多抗病机制导致Ca2+可渗透孔的形成,并且Ca2+内流的光遗传激活足以触发免疫反应。这篇综述强调Ca2+解码,即不同的细胞内蛋白如何解释Ca2+信号来驱动细胞反应。“Ca2+反应性”状态-由不同解码器的不同敏感性和额外的致敏机制定义-有助于免疫调节,可能包括模式和效应触发的免疫途径的相互增强。此外,免疫信号的“引物-旁观者”模型在这个解码框架内被解释。在这里,被感染的细胞被提议通过来自抵抗体孔隙的强Ca2+信号进入引物(PRIMER)免疫状态,而邻近的旁观者细胞对来自其邻居的扩散信号分子作出反应。通过这种空间安排,实现了细胞自主(自分泌)反应和非自主(旁分泌或内分泌)信号之间的协调,从而实现了植物组织间强大的免疫传播。通过这种Ca2+“感觉和敏感性”范式构建植物免疫,提供了对免疫系统鲁棒性的见解,并可能为未来抗病,气候适应型作物的开发确定潜在目标。
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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 Q1 PLANT SCIENCES Pub Date : 2025-08-25 DOI: 10.1016/j.pbi.2025.102780
Aida Maric , Advait Agashe , Johanna Söntgerath , Sjon Hartman
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.
乙烯是一种重要的植物激素,控制着过多的植物发育和胁迫反应。因此,乙烯信号的产生和发展必须受到严格的时空控制。本文综述了在理解表观遗传机制如何控制乙烯生物合成和信号传导,以及乙烯介导的表观遗传修饰子如何反过来控制基因表达和生物过程方面的最新里程碑。我们讨论了乙烯控制的组蛋白乙酰化对乙烯信号进展至关重要的中心机制。此外,我们概述了广泛的表观遗传机制如何控制乙烯介导的发育和胁迫反应,重点是水果成熟。最后,提出了乙烯信号在植物表观遗传机制中的整合研究方向和有待解决的问题。
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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 Q1 PLANT SCIENCES Pub Date : 2025-08-16 DOI: 10.1016/j.pbi.2025.102766
Camila Goldy , Virginia Barrera , Mariana Sotelo-Silveira , Ramiro E. Rodriguez
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 Arabidopsis thaliana 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.
主要分布在器官纵轴的弥漫性细胞扩增对根器官的生长有显著的促进作用。根细胞的扩张是一个多样化、可塑性和动态的过程,每个细胞根据其发育阶段和不同的环境条件以特定的速度和方向扩张,帮助塑造根系结构。在这篇综述中,我们将重点介绍拟南芥分生组织和有丝分裂后根细胞的细胞扩增模式和大小,并评估细胞扩增发生所需转变的最新进展。我们还详细阐述了控制力量的基因表达程序,决定细胞扩增的生化和分子机制,最后,这一过程的大小和分布的变化如何促进根对环境的适应。
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引用次数: 0
Metabolic innovations: The study of the less ordinary 代谢创新:对不平凡事物的研究
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-08-13 DOI: 10.1016/j.pbi.2025.102767
Alisdair R. Fernie, Shijuan Yan
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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 Q1 PLANT SCIENCES Pub Date : 2025-08-05 DOI: 10.1016/j.pbi.2025.102762
Hongyuan Zhang, Trang Dang, Lucia Piro, Diana Santelia
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.
在波动光照条件下,设计快速的气孔响应来改善气孔导度与碳同化之间的协调,对于提高作物产量和节约水分至关重要。为了确定有希望的工程目标,我们应用机器学习模型来分析来自不同植物谱系的已发表数据,以揭示驱动气孔打开速度自然变化的主要因素。我们强调了保护细胞淀粉在整合和调节这些因素中的多种作用,并建议淀粉作为一个以前被忽视的优化气孔功能的目标。
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引用次数: 0
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Current opinion in plant biology
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