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Authors: Jazmine L. Humphreys, Christine A. Beveridge and Miloš Tanurdžić.
bioRxiv (2023)
Abstract: "Strigolactones (SL) function as plant hormones in control of multiple aspects of plant development. Regulation of gene expression by SL is a critical component of SL function. Immediate early gene regulation by SL remains unexplored due to difficulty in dissecting early from late gene expression responses to SL in whole plants. We used leaf-derived Arabidopsis protoplasts to explore early (5-180 minutes) changes in gene expression induced by SL by employing RNA-seq and ATAC-seq. We discovered over 1500 genes regulated by SL as early as 20 minutes, and up to 3669 genes across the entire time course of the experiment, indicative of rapid, dynamic regulation of gene expression in response to SLs. We identified 1447 regions of changing chromatin accessibility in response to SL that are likely to harbour SL cis-regulatory elements and cognate candidate trans-acting factors regulated early by SL. Importantly, we discovered that this extensive transcriptomic reprogramming requires the SYD-containing SWI/SNF chromatin remodelling complex(es) and regulates other chromatin remodellers. This study therefore provides the first evidence that SL signalling requires regulation of chromatin accessibility, and it identifies previously unknown transcriptional targets of strigolactones."
Authors: Fu-Xiang Wang, Guan-Dong Shang and Jia-Wei Wang.
Trends in Plant Science (2022)
Highlights: Chromatin status influences cellular competence for somatic embryogenesis. Auxin induces the acquisition of totipotency through altering chromatin accessibility and the transcriptome. The LEC2–WOX2/3 axis serves as a molecular link between totipotency-related transcription factor genes and early embryonic development pathway.
Abstract: "Genome-editing technologies have advanced in recent years but designing future crops remains limited by current methods of improving somatic embryogenesis (SE) capacity. In this Opinion, we provide an update on the molecular event by which the phytohormone auxin promotes the acquisition of plant cell totipotency through evoking massive changes in transcriptome and chromatin accessibility. We propose that the chromatin states and individual totipotency-related transcription factors (TFs) from disparate gene families organize into a hierarchical gene regulatory network underlying SE. We conclude with a discussion of the practical paths to probe the cellular origin of the somatic embryo and the epigenetic landscape of the totipotent cell state in the era of single-cell genomics."
Authors: Alice Lambolez, Ayako Kawamura, Tatsuya Takahashi, Bart Rymen, Akira Iwase, David S. Favero, Momoko Ikeuchi, Takamasa Suzuki, Sandra Cortijo, Katja E. Jaeger, Philip A Wigge and Keiko Sugimoto.
Plant and Cell Physiology (2022)
Abstract: "Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we find that warm temperature promotes both callus formation and shoot regeneration in Arabidopsis thaliana. We show that such an increase in shoot regenerative capacity at higher temperatures correlates with the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1) encoding a transcription factor involved in shoot meristem formation and YUCCAs (YUCs) encoding auxin biosynthesis enzymes. ChIP-sequencing analyses further reveal that histone variant H2A.Z is enriched on these loci at 17°C, while its occupancy is reduced by an increase in ambient temperature to 27°C. Moreover, we provide genetic evidence to demonstrate that H2A.Z acts as a repressor of de novo shoot organogenesis since H2A.Z-depleted mutants display enhanced shoot regeneration. This study thus uncovers a new chromatin-based mechanism that influences hormone-induced regeneration and additionally highlights incubation temperature as a key parameter for optimizing in vitro tissue culture."
Authors: Wei Zong, Junghyun Kim, Yogendra Bordiya, Hong Qiao and Sibum Sung.
New Phytologist (2022)
Abstract: "Polycomb dictates developmental programs in higher eukaryotes, including flowering plants. A phytohormone, Abscisic acid (ABA), plays a pivotal role in seed and seedling development and mediates responses to multiple environmental stresses, such as salinity and drought. In this study, we show that ABA affects the Polycomb Repressive Complex 2 (PRC2)-mediated Histone H3 Lys 27 trimethylation (H3K27me3) through VIN3-LIKE1/VERNALIZATION 5 (VIL1/VRN5) to fine-tune the timely repression of ABSCISIC ACID INSENSITIVE 3 (ABI3) and ABSCISIC ACID INSENSITIVE 4 (ABI4) in Arabidopsis thaliana. vil1 mutants exhibit hypersensitivity to ABA during early seed germination and show enhanced drought tolerance. Our study revealed that the ABA signaling pathway utilizes a facultative component of the chromatin remodeling complex to demarcate the level of expression of ABA-responsive genes.
Authors: Lian-Yu Wu, Guan-Dong Shang, Fu-Xiang Wang, Jian Gao, Mu-Chun Wan, Zhou-Geng Xu and Jia-Wei Wang.
Developmental Cell (2022)
Editor's view: Examining chromatin states during shoot regeneration in Arabidopsis, Wu, Shang et al. reveal how auxin and cytokinin dismantle somatic chromatin and establish an epigenetic state compatible with pluripotency. They present a catalog of regulatory sequences temporally associated with cell fate transition and identify transcription factors involved in shoot regeneration.
Highlights: • The dynamic chromatin state landscape during shoot regeneration is revealed • Collapse of pluripotency in the absence of cytokinin signaling • Generation of a catalog of regulatory sequences during shoot regeneration • A cohort of transcription factors involved in shoot regeneration is outlined
Abstract: "Shoot regeneration is mediated by the sequential action of two phytohormones, auxin and cytokinin. However, the chromatin regulatory landscapes underlying this dynamic response have not yet been studied. In this study, we jointly profiled chromatin accessibility, histone modifications, and transcriptomes to demonstrate that a high auxin/cytokinin ratio environment primes Arabidopsis shoot regeneration by increasing the accessibility of the gene loci associated with pluripotency and shoot fate determination. Cytokinin signaling not only triggers the commitment of the shoot progenitor at later stages but also allows chromatin to maintain shoot identity genes at the priming stage. Our analysis of transcriptional regulatory dynamics further identifies a catalog of regeneration cis-elements dedicated to cell fate transitions and uncovers important roles of BES1, MYC, IDD, and PIF transcription factors in shoot regeneration. Our results, thus, provide a comprehensive resource for studying cell reprogramming in plants and provide potential targets for improving future shoot regeneration efficiency."
Authors: Elzbieta Sarnowska, Szymon Kubala, Pawel Cwiek, Sebastian Sacharowski, Paulina Oksinska, Jaroslaw Steciuk, Magdalena Zaborowska, Jakub M. Szurmak, Roman Dubianski, Anna Maassen, Malgorzata Stachowiak, Bruno Huettel, Monika Ciesla, Klaudia Nowicka, Anna T. Rolicka, Saleh Alseekh, Ernest Bucior, Rainer Franzen, Anna Klepacz, Malgorzata Anna Domagalska, Samija Amar, Alisdair R. Fernie, Seth J. Davis and Tomasz J. Sarnowski.
bioRxiv (2021)
Abstract: "The Arabidopsis ERECTA family (ERf) of leucine-rich repeat receptor-like kinases (LRR-RLKs), comprising ERECTA (ER), ERECTA-LIKE 1 (ERL1) and ERECTA-LIKE 2 (ERL2), control epidermal patterning, inflorescence architecture, stomata development, and hormonal signaling. Here we show that the er/erl1/erl2 triple mutant exhibits impaired gibberellin (GA) biosynthesis and perception alongside broad transcriptional changes. ERf proteins interact in the nucleus, via kinase domains, with the SWI3B subunit of the SWI/SNF chromatin remodeling complex (CRCs). The er/erl1/erl2 triple mutant exhibits reduced SWI3B protein level and affected nucleosomal chromatin structure. The ER kinase phosphorylates SWI3B in vitro, and the inactivation of all ERf proteins leads to the decreased phosphorylation of SWI3B protein in vivo. Correlation between DELLA overaccumulation and SWI3B proteasomal degradation together with the physical interaction of SWI3B with DELLA proteins explain the lack of RGA accumulation in the GA- and SWI3B-deficient erf mutant plants. Co-localization of ER and SWI3B on GID1 (GIBBERELLIN INSENSITIVE DWARF 1) DELLA target gene promoter regions and abolished SWI3B binding to GID1 promoters in er/erl1/erl2 plants supports the conclusion that ERf-SWI/SNF CRC interaction is important for transcriptional control of GA receptors. Thus, the involvement of ERf proteins in transcriptional control of gene expression, and observed similar features for human HER2 (Epidermal Growth Family Receptor-member), indicate an exciting target for further studies of evolutionarily conserved non-canonical functions of eukaryotic membrane receptors."
Authors: Deyue Yang, Fengli Zhao, Danling Zhu, Xi Chen, Xiangxiong Kong, Yufeng Wu, Min Chen, Jiamu Du, Li-jia Qu and Zhe Wu.
bioRxiv (2021)
Abstract: "Seed germination represents a major developmental switch in plants that is vital to agricultural, but how this process is controlled at the chromatin level remains obscure. Here we demonstrate that successful germination in Arabidopsis requires a chromatin mechanism that progressively silences NCED6, which encodes a rate-limiting enzyme for abscisic acid (ABA) biosynthesis, through the cooperative action of the RNA-binding protein RZ-1 and the polycomb repressive complex 2 (PRC2). Simultaneous inactivation of RZ-1 and PRC2 blocks germination and synergistically depresses NCEDs and hundreds of genes. At NCED6, by promoting H3 deacetylation and suppressing H3K4me3, RZ-1 facilitates transcriptional silencing and also a H3K27me3 accumulation process that occurs during seed germination and early seedling growth. Genome-wide analysis reveals RZ-1 is preferentially required for transcriptional silencing of many PRC2 targets early during seed germination when H3K27me3 is not yet established. We propose RZ-1 confers a novel silencing mechanism to compensate and coordinate with PRC2. Our work highlights the progressive chromatin silencing of ABA biosynthesis genes via energized action of the RNA-binding protein RZ1 and PRC2, which is vital for seed germination."
Authors: Ashish Kumar Srivastava, Jisha Suresh Kumar and Penna Suprasanna.
Biological Reviews (2021)
Abstract: "Seed priming is a pre‐germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of ‘stress memory’ in which exposure to a sub‐lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly‐ethylene glycol, CaCl2 and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)–abscisic acid (ABA)–heme regulatory module, ABA–gibberellic acid antagonism and nucleus–organelle communication are detailed. We propose that both seed priming and stress memory invoke a ‘bet‐hedging’ strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR‐responsive varieties and the development of dual/multiple‐benefit SPRs, is proposed for enhancing SPR‐mediated agricultural productivity worldwide."
Authors: Zicong Li, Xiao Luo, Yang Ou, Huijun Jiao, Li Peng, Xing Fu, Alberto P. Macho, Renyi Liu and Yuehui He.
Molecular Plant (2021)
Abstract: "Jasmonate (JA) regulates various aspects of plant growth and development and stress responses, with prominent roles in male reproductive development and defenses against herbivores and necrotrophic pathogens. JASMONATE-ZIM DOMAIN (JAZ) proteins are key regulators in the JA signaling pathway and function to repress the expression of JA-responsive genes. Here, we show that JAZ proteins directly interact with several chromatin-associated Polycomb proteins to mediate repressive chromatin modifications at part of JA-responsive genes and thus their transcriptional repression in Arabidopsis. Genetic analyses revealed that the developmental defects, including anther and pollen abnormalities resulting from loss or block of JA signaling, were partially rescued by loss of Polycomb protein-mediated chromatin silencing (Polycomb repression). We further found that JAZ-mediated transcriptional repression requires Polycomb proteins at four key regulatory loci in anther and pollen development. Analysis of genome-wide occupancy of a Polycomb factor and transcriptome reprogramming in response to JA reveals that Polycomb repression is involved in the repression of various JA-responsive genes. Taken together, our study reveals an important chromatin-based mechanism for JAZ-mediated transcriptional repression and JA signaling in plants."
Authors: Yang Bi, Zhiping Deng, Weimin Ni, Ruben Shrestha, Dasha Savage, Thomas Hartwig, Sunita Patil, Su Hyun Hong, Zhenzhen Zhang, Juan A. Oses-Prieto, Kathy H. Li, Peter H. Quail, Alma L. Burlingame, Shou-Ling Xu and Zhi-Yong Wang.
Nature Communications (2021)
Editor's view: AtACINUS is an Arabidopsis homolog of a mammalian splicing regulator and previously found to be O-GlcNAcyated. Here Bi et al. characterize the interactors and targets of AtACINUS, show it is required for development and stress responses and provide evidence that its O-glycosylation affects alternative splicing.
Abstract: "O-GlcNAc modification plays important roles in metabolic regulation of cellular status. Two homologs of O-GlcNAc transferase, SECRET AGENT (SEC) and SPINDLY (SPY), which have O-GlcNAc and O-fucosyl transferase activities, respectively, are essential in Arabidopsis but have largely unknown cellular targets. Here we show that AtACINUS is O-GlcNAcylated and O-fucosylated and mediates regulation of transcription, alternative splicing (AS), and developmental transitions. Knocking-out both AtACINUS and its distant paralog AtPININ causes severe growth defects including dwarfism, delayed seed germination and flowering, and abscisic acid (ABA) hypersensitivity. Transcriptomic and protein-DNA/RNA interaction analyses demonstrate that AtACINUS represses transcription of the flowering repressor FLC and mediates AS of ABH1 and HAB1, two negative regulators of ABA signaling. Proteomic analyses show AtACINUS’s O-GlcNAcylation, O-fucosylation, and association with splicing factors, chromatin remodelers, and transcriptional regulators. Some AtACINUS/AtPININ-dependent AS events are altered in the sec and spy mutants, demonstrating a function of O-glycosylation in regulating alternative RNA splicing. AtACINUS is an Arabidopsis homolog of a mammalian splicing regulator and previously found to be O-GlcNAcyated. Here Bi et al. characterize the interactors and targets of AtACINUS, show it is required for development and stress responses and provide evidence that its O-glycosylation affects alternative splicing."
Authors: Choonkyun Jung, Nguyen Hoai Nguyen and Jong-Joo Cheong.
International Journal of Molecular Sciences (2020)
Abstract: "The plant hormone abscisic acid (ABA) triggers cellular tolerance responses to osmotic stress caused by drought and salinity. ABA controls the turgor pressure of guard cells in the plant epidermis, leading to stomatal closure to minimize water loss. However, stomatal apertures open to uptake CO2 for photosynthesis even under stress conditions. ABA modulates its signaling pathway via negative feedback regulation to maintain plant homeostasis. In the nuclei of guard cells, the clade A type 2C protein phosphatases (PP2Cs) counteract SnRK2 kinases by physical interaction, and thereby inhibit activation of the transcription factors that mediate ABA-responsive gene expression. Under osmotic stress conditions, PP2Cs bind to soluble ABA receptors to capture ABA and release active SnRK2s. Thus, PP2Cs function as a switch at the center of the ABA signaling network. ABA induces the expression of genes encoding repressors or activators of PP2C gene transcription. These regulators mediate the conversion of PP2C chromatins from a repressive to an active state for gene transcription. The stress-induced chromatin remodeling states of ABA-responsive genes could be memorized and transmitted to plant progeny; i.e., transgenerational epigenetic inheritance. This review focuses on the mechanism by which PP2C gene transcription modulates ABA signaling."
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Authors: Wenxing Chen, Yosuke Tamada, Hisayo Yamane, Miwako Matsushita, Yutaro Osako, Mei Gao-Takai, Zhengrong Luo and Ryutaro Tao.
The Plant Journal (2022)
Abstract: "Bud dormancy helps woody perennials survive winter and activate robust plant development in the spring. For apple (Malus × domestica), short-term chilling induces bud dormancy in autumn, then prolonged chilling leads to dormancy release and a shift to a quiescent state in winter, with subsequent warm periods promoting bud break in spring. Epigenetic regulation contributes to seasonal responses such as vernalization. However, how histone modifications integrate seasonal cues and internal signals during bud dormancy in woody perennials remains largely unknown. Here, we show that H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. The global changes in gene expression strongly correlated with changes in H3K4me3, but not H3K27me3. High expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes, key regulators of dormancy, in autumn was associated with high H3K4me3 levels. In addition, known DAM/SHORT VEGETATIVE PHASE (SVP) target genes significantly overlapped with H3K4me3-modified genes as bud dormancy progressed. These data suggest that H3K4me3 contributes to the central dormancy circuit, consisting of DAM/SVP and abscisic acid (ABA), in autumn. In winter, the lower expression and H3K4me3 levels at DAMs and gibberellin metabolism genes control chilling-induced release of dormancy. Warming conditions in spring facilitate the expression of genes related to phytohormones, the cell cycle, and cell wall modification by increasing H3K4me3 toward bud break. Our study also revealed that activation of auxin and repression of ABA sensitivity in spring are conditioned at least partly through temperature-mediated epigenetic regulation in winter."
Author: Mariana A. S. Artur.
The Plant Cell (2022)
Excerpts: "In a new study, Deyue Yang, Fengli Zhao and colleagues (2022) identified the role of the RNA-binding protein RZ-1 in a novel chromatin silencing mechanism that influences seed germination."
"The authors found that mutation of the genes encoding RZ-1B and RZ-1C proteins (rz-1b rz-1c) leads to delayed seed germination and increased accumulation of the hormone abscisic acid (ABA). ABA is produced during seed development to inhibit precocious germination and is a major regulator of seed dormancy (Hilhorst and Karssen, 1992). To investigate the causes of altered ABA accumulation, the authors quantified gene expression in rz-1b rz-1c mutants and in a complementation line (RZ-1Cpro:GFP-RZ-1C) and found that several ABA biosynthesis and signalling genes (e.g., NCED6 and ABI3) were upregulated in the mutants. The authors then crossed rz-1b rz-1c with several ABA-related mutants and observed full recovery of the delayed germination phenotype in the mutant (Figure). This indicated that RZ-1 controls germination through silencing of ABA biosynthesis and signalling genes. "
Authors: Ambreen Khan, Varisha Khan, Khyati Pandey, Sudhir Kumar Sopory and Neeti Sanan-Mishra.
Frontiers in Plant Science (2022)
Abstract: "Plants can adapt to different environmental conditions and can survive even under very harsh conditions. They have developed elaborate networks of receptors and signaling components, which modulate their biochemistry and physiology by regulating the genetic information. Plants also have the abilities to transmit information between their different parts to ensure a holistic response to any adverse environmental challenge. One such phenomenon that has received greater attention in recent years is called stress priming. Any milder exposure to stress is used by plants to prime themselves by modifying various cellular and molecular parameters. These changes seem to stay as memory and prepare the plants to better tolerate subsequent exposure to severe stress. In this review, we have discussed the various ways in which plants can be primed and illustrate the biochemical and molecular changes, including chromatin modification leading to stress memory, with major focus on thermo-priming. Alteration in various hormones and their subsequent role during and after priming under various stress conditions imposed by changing climate conditions are also discussed."
Authors: Stacey A. Vincent, Jong-Myong Kim, Imma Pérez-Salamó, Taiko Kim To, Chieko Torii, Junko Ishida, Maho Tanaka, Takaho A. Endo, Prajwal Bhat, Paul F. Devlin, Motoaki Seki and Alessandra Devoto.
BMC Biology (2022)
Abstract: "Background - Jasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive. Results - We performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses. Conclusions - The findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges."
Authors: Qingshuai Chen, Jing Zhang and Gang Li.
Trends in Plant Science (2022)
Highlights: Sugars act as signaling molecules to control plant growth and development through the regulation of gene expression and metabolic processes. Direct and indirect sugar responses are accompanied by changes in the chromatin landscape. Epigenetic modifications, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation, intertwine to enrich the sugar regulatory network. Plants adapt to variable environments through flexible and diverse epigenetic mechanisms that mediate the perception and transduction of sugar signals. Epigenetic modifiers integrate various inputs to coordinate sugar signals with other internal and external signals during plant growth and development.
Abstract: "In eukaryotes, dynamic chromatin states are closely related to changes in gene expression. Epigenetic modifications help plants adapt to their ever-changing environment by modulating gene expression via covalent modification at specific sites on DNA or histones. Sugars provide energy, but also function as signaling molecules to control plant growth and development. Various epigenetic modifications participate in sensing and transmitting sugar signals. Here we summarize recent progress in uncovering the epigenetic mechanisms involved in sugar signal transduction, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation. We also highlight changes in chromatin marks when crosstalk occurs between sugar signaling and the light, temperature, and phytohormone signaling pathways, and describe potential questions and approaches for future research."
Authors: Liping Liu, Mengnan Chai, Youmei Huang, Jingang Qi, Wenhui Zhu, Xinpeng Xi, Fangqian Chen, Yuan Qin and Hanyang Cai.
iScience (2021)
Highlights • SDG2 genetically interacts with the SWR1-ERECTA pathway in inflorescence development • SWR1-ERECTA pathway is required to enrich H2A.Z and H3K4me3 at auxin-related genes • H2A.Z histone variant enrichment was regulated by SDG2
Abstract: "Inflorescence architecture is diverse in flowering plants, and two determinants of inflorescence architecture are the inflorescence meristem and pedicel length. Although the ERECTA (ER) signaling pathway, in coordination with the SWR1 chromatin remodeling complex, regulates inflorescence architecture with subsequent effects on pedicel elongation, the mechanism underlying SWR1-ER signaling pathway regulation of inflorescence architecture remains unclear. This study determined that SDG2 genetically interacts with the SWR1-ER signaling pathways in regulating inflorescence architecture. Transcriptome results showed that auxin might potentially influence inflorescence growth mediated by SDG2 and SWR1-ER pathways. SWR1 and ER signaling are required to enrich H2A.Z histone variant and SDG2 regulated SDG2-mediated H3K4me3 histone modification at auxin-related genes and H2A.Z histone variant enrichment. Our study shows how the regulation of inflorescence architecture is mediated by SDG2 and SWR1-ER, which affects auxin hormone signaling pathways."
Authors: Isabel Cristina Vélez-Bermúdez and Wolfgang Schmidt.
bioRxiv (2021)
Abstract: "Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE 6 (AL6), a bona fide histone reader that preferentially binds trimethylated lysin 4 on histone 3 (H3K4me3), is critical for recalibration of cellular phosphate (Pi) homeostasis and root hair elongation under Pi-deficient conditions. Here, we demonstrate that AL6 is also involved in the response of Arabidopsis seedlings to jasmonic acid (JA) during skotomorphogenesis, possibly by modulating chromatin dynamics that affect the transcriptional regulation of JA-responsive genes. Dark-grown al6 seedlings showed a compromised reduction in hypocotyl elongation upon exogenously supplied JA, a response that was calibrated by the availability of Pi in the growth medium. A comparison of protein profiles between wild-type and al6 mutant seedlings using a quantitative Chromatin Enrichment for Proteomics (ChEP) approach, that we modified for plant tissue and designated ChEP-P (ChEP in Plants), yielded a comprehensive suite of chromatin-associated proteins and candidates that may be causative for the mutant phenotype. Altered abundance of proteins involved in chromatin organization in al6 seedlings suggests a role of AL6 in coordinating the deposition of histone variants upon perception of internal or environmental stimuli."
Author: Mark Zander.
Molecular Plant (2021)
Excerpts: "To prevent TF-induced transcriptional gene activation, JAZs use multiple strategies. Here, I will discuss this versatile repressive repertoire of JAZ proteins, especially in light of Li et al. (Li et al., 2021) new findings of a JAZ-mediated repression mechanism that operates through the direct engagement of PRC2 (Polycomb Repressive Complex 2)."
" Li et al. (Li et al., 2021) discovered in this issue that seven (JAZ1, JAZ3, JAZ4, JAZ6, JAZ8, JAZ9 and JAZ10) out of the 13 Arabidopsis JAZ proteins as well as the adaptor protein NINJA can interact with the H3K27me3 reader LHP1 and the PRC2 structural core subunit EMF2 (EMBRYONIC FLOWER 2) in yeast and in planta."
"The molecular determinants for the individual modes of repression including their dynamics are unclear at this point but a mixture of stress, developmental, tissue and locus-specific contexts can be envisioned. Future research is needed to shed more light on this intriguing repressive repertoire of JAZs."
Authors: Kai Chen, Kangxi Du, Yichen Shi, Liufan Yin, Wen‐Hui Shen, Yu Yu, Bing Liu and Aiwu Dong.
New Phytologist (2021)
Abstract: "Chromatin modifications play important roles in plant adaptation to abiotic stresses, but the precise function of histone H3 lysine 36 (H3K36) methylation in drought tolerance remains poorly evaluated. Here, we report that SDG708, a specific H3K36 methyltransferase, functions as a positive regulator of drought tolerance in rice. SDG708 promoted abscisic acid (ABA) biosynthesis by directly targeting and activating the crucial ABA biosynthesis genes NINE‐CIS‐EPOXYCAROTENOID DIOXYGENASE 3 (OsNCED3) and NINE‐CIS‐EPOXYCAROTENOID DIOXYGENASE 5 (OsNCED5). Additionally, SDG708 induced hydrogen peroxide accumulation in the guard cells and promoted stomatal closure to reduce water loss. Overexpression of SDG708 concomitantly enhanced rice drought tolerance and increased grain yield under normal and drought stress conditions. Thus, SDG708 is potentially useful as an epigenetic regulator in breeding for grain yield improvement."
Authors: Galina Smolikova, Tatiana Leonova, Natalia Vashurina, Andrej Frolov and Sergei Medvedev.
International Journal of Molecular Sciences (2020)
Abstract: "Desiccation tolerance appeared as the key adaptation feature of photoautotrophic organisms for survival in terrestrial habitats. During the further evolution, vascular plants developed complex anatomy structures and molecular mechanisms to maintain the hydrated state of cell environment and sustain dehydration. However, the role of the genes encoding the mechanisms behind this adaptive feature of terrestrial plants changed with their evolution. Thus, in higher vascular plants it is restricted to protection of spores, seeds and pollen from dehydration, whereas the mature vegetative stages became sensitive to desiccation. During maturation, orthodox seeds lose up to 95% of water and successfully enter dormancy. This feature allows seeds maintaining their viability even under strongly fluctuating environmental conditions. The mechanisms behind the desiccation tolerance are activated at the late seed maturation stage and are associated with the accumulation of late embryogenesis abundant (LEA) proteins, small heat shock proteins (sHSP), non-reducing oligosaccharides, and antioxidants of different chemical nature. The main regulators of maturation and desiccation tolerance are abscisic acid and protein DOG1, which control the network of transcription factors, represented by LEC1, LEC2, FUS3, ABI3, ABI5, AGL67, PLATZ1, PLATZ2. This network is complemented by epigenetic regulation of gene expression via methylation of DNA, post-translational modifications of histones and chromatin remodeling. These fine regulatory mechanisms allow orthodox seeds maintaining desiccation tolerance during the whole period of germination up to the stage of radicle protrusion. This time point, in which seeds lose desiccation tolerance, is critical for the whole process of seed development."
Authors: Li Ya Ma, Xiao Yan Zhai, Yu Xin Qiao, Ai Ping Zhang, Nan Zhang, Jintong Liu and Hong Yang.
Environmental Pollution (2020)
Highlights: • OsCOI1a is a critical component of the jasmonate-signaling pathway. • Overexpressing OsCOI1a resisted to ATZ toxicity and reduced ATZ concentration. • More ATZ metabolites were detected in overexpressing OsCOI1a rice. • The OsCOI1a expression was enhanced by DNA hypomethylation under ATZ stress.
Abstract: "Developing a biotechnical system with rapid degradation of pesticide is critical for reducing environmental, food security and health risks. Here, we investigated a novel epigenetic mechanism responsible for the degradation of the pesticide atrazine (ATZ) in rice crops mediated by the key component CORONATINE INSENSITIVE 1a (OsCOI1a) in the jasmonate-signaling pathway. OsCOI1a protein was localized to the nucleus and strongly induced by ATZ exposure. Overexpression of OsCOI1a (OE) significantly conferred resistance to ATZ toxicity, leading to the improved growth and reduced ATZ accumulation (particularly in grains) in rice crops. HPLC/Q-TOF-MS/MS analysis revealed increased ATZ-degraded products in the OE plants, suggesting the occurrence of vigorous ATZ catabolism. Bisulfite-sequencing and chromatin immunoprecipitation assays showed that ATZ exposure drastically reduced DNA methylation at CpG context and histone H3K9me2 marks in the upstream of OsCOI1a. The causal relationships between the DNA demethylation (hypomethylatioin), OsCOI1a expression and subsequent detoxification and degradation of ATZ in rice and environment were well established by several lines of biological, genetic and chemical evidence. Our work uncovered a novel regulatory mechanism implicated in the defense linked to the epigenetic modification and jasmonate signaling pathway. It also provided a modus operandi that can be used for metabolic engineering of rice to minimize amounts of ATZ in the crop and environment.
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