1
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Guo J, He XJ. Composition and function of plant chromatin remodeling complexes. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102613. [PMID: 39116678 DOI: 10.1016/j.pbi.2024.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/10/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024]
Abstract
ATP-dependent chromatin remodelers play a crucial role in modifying chromatin configuration by utilizing the energy of ATP hydrolysis. They are involved in various processes, including transcription, DNA replication, and maintaining genome stability. These remodeling remodelers usually form multi-subunit chromatin remodeling complexes in eukaryotes. In plants, chromatin remodeling complexes have diverse functions in regulating plant development and stress response. Recent studies have conducted extensive research on plant chromatin remodeling complexes. This review focuses on recent advances in the classification and composition of plant chromatin remodeling complexes, the protein-protein interactions within the complexes, their impact on chromatin configuration, and their interactions with chromatin modifications and transcription factors.
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Affiliation(s)
- Jing Guo
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China.
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2
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Baile F, Calonje M. Dynamics of polycomb group marks in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102553. [PMID: 38776572 DOI: 10.1016/j.pbi.2024.102553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/08/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Polycomb Group (PcG) histone-modifying system is key in maintaining gene repression, providing a mitotically heritable cellular memory. Nevertheless, to allow plants to transition through distinct transcriptional programs during development or to respond to external cues, PcG-mediated repression requires reversibility. Several data suggest that the dynamics of PcG marks may vary considerably in different cell contexts; however, how PcG marks are established, maintained, or removed in each case is far from clear. In this review, we survey the knowns and unknowns of the molecular mechanisms underlying the maintenance or turnover of PcG marks in different cell stages.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain.
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3
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Wang W, Sung S. Chromatin sensing: integration of environmental signals to reprogram plant development through chromatin regulators. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4332-4345. [PMID: 38436409 PMCID: PMC11263488 DOI: 10.1093/jxb/erae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Chromatin regulation in eukaryotes plays pivotal roles in controlling the developmental regulatory gene network. This review explores the intricate interplay between chromatin regulators and environmental signals, elucidating their roles in shaping plant development. As sessile organisms, plants have evolved sophisticated mechanisms to perceive and respond to environmental cues, orchestrating developmental programs that ensure adaptability and survival. A central aspect of this dynamic response lies in the modulation of versatile gene regulatory networks, mediated in part by various chromatin regulators. Here, we summarized current understanding of the molecular mechanisms through which chromatin regulators integrate environmental signals, influencing key aspects of plant development.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
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4
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Liu Q, Ma W, Chen R, Li S, Wang Q, Wei C, Hong Y, Sun H, Cheng Q, Zhao J, Kang J. Multiome in the Same Cell Reveals the Impact of Osmotic Stress on Arabidopsis Root Tip Development at Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308384. [PMID: 38634607 PMCID: PMC11199978 DOI: 10.1002/advs.202308384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/27/2024] [Indexed: 04/19/2024]
Abstract
Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to directly capture the relationships and dynamics between different layers of molecular information within the same cells. While advanced algorithm facilitates merging scRNA-seq and scATAC-seq datasets, accurate data integration remains a challenge, particularly when investigating cell-type-specific TRNs. By examining gene expression and chromatin accessibility simultaneously in 16,670 Arabidopsis root tip nuclei, the TRNs are reconstructed that govern root tip development under osmotic stress. In contrast to commonly used computational integration at cell-type level, 12,968 peak-to-gene linkage is captured at the bona fide single-cell level and construct TRNs at an unprecedented resolution. Furthermore, the unprecedented datasets allow to more accurately reconstruct the coordinated changes of gene expression and chromatin states during cellular state transition. During root tip development, chromatin accessibility of initial cells precedes gene expression, suggesting that changes in chromatin accessibility may prime cells for subsequent differentiation steps. Pseudo-time trajectory analysis reveal that osmotic stress can shift the functional differentiation of trichoblast. Candidate stress-related gene-linked cis-regulatory elements (gl-cCREs) as well as potential target genes are also identified, and uncovered large cellular heterogeneity under osmotic stress.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Wei Ma
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Ruiying Chen
- BGI ResearchBeijing102601China
- BGI ResearchShenzhen518083China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | | | - Qifan Wang
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Cai Wei
- BGI ResearchBeijing102601China
| | - Yiguo Hong
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
| | - Hai‐Xi Sun
- BGI ResearchBeijing102601China
- BGI ResearchShenzhen518083China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Qi Cheng
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Jingmin Kang
- BGI ResearchBeijing102601China
- BGI ResearchShenzhen518083China
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5
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Xu H, Chen X, Zeng G, Qin X, Deng Z, Cheng W, Shen X, Hu Y. Unveiling common and specific features of the COMPASS-like complex in sorghum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108709. [PMID: 38744082 DOI: 10.1016/j.plaphy.2024.108709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
The COMPASS-like complex, responsible for depositing H3K4 methylation, exhibits a conserved composition across yeast, plants, and animals, with functional analysis highlighting its crucial roles in plant development and stress response. In this study, we identified nine genes encoding four subunits of the COMPASS-like complex through homologous search. Phylogenetic analysis revealed the presence of two additional ASH2 genes in the sorghum genome, specifically expressed in endosperms, suggesting the formation of a unique COMPASS-like complex in sorghum endosperms. Y2H and BiFC protein-protein interaction tests demonstrated the interaction between SbRbBP5 and SbASH2A/B/C, while the association between other subunits appeared weak, possibly due to sequence variations in SbWDR5 or synergistic interactions among COMPASS-like complex subunits. The interaction between ATX1 and the C-Terminal Domain (CTD) of Pol II, reported in Arabidopsis, was not detected in sorghum. However, we made the novel discovery of transcriptional activation activity in RbBP5, which is conserved in sorghum, rice, and Arabidopsis, providing valuable insights into the mechanism by which the COMPASS-like complex regulates gene expression in plants.
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Affiliation(s)
- Huan Xu
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China; Jingchu University of Technology, Jingmen, Hubei, 448000, China
| | - Xiaoliang Chen
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Gongjian Zeng
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Xiner Qin
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Zhuying Deng
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Wenhan Cheng
- Jingchu University of Technology, Jingmen, Hubei, 448000, China
| | - Xiangling Shen
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China.
| | - Yongfeng Hu
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China.
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6
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Wu Z, Gao H, Liu Z. COMPASS core subunits MpSet1 and MpSwd3 regulate Monascus pigments synthesis in Monascus purpureus. J Basic Microbiol 2024; 64:e2300686. [PMID: 38362934 DOI: 10.1002/jobm.202300686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
In eukaryotes, methylation of histone H3 at lysine 4 (H3K4me) catalyzed by the complex of proteins associated with Set1 (COMPASS) is crucial for the transcriptional regulation of genes and the development of organisms. In Monascus, the functions of COMPASS in establishing H3K4me remain unclear. This study first identified the conserved COMPASS core subunits MpSet1 and MpSwd3 in Monascus purpureus and confirmed their roles in establishing H3K4me2/3. Loss of MpSet1 and MpSwd3 resulted in slower growth and development and inhibited the formation of cleistothecia, ascospores, and conidia. The loss of these core subunits also decreased the production of extracellular and intracellular Monascus pigments (MPs) by 94.2%, 93.5%, 82.7%, and 82.5%, respectively. In addition, RNA high-throughput sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) showed that the loss of MpSet1 and MpSwd3 altered the expression of 2646 and 2659 genes, respectively, and repressed the transcription of MPs synthesis-related genes. In addition, the ΔMpset1 and ΔMpswd3 strains demonstrated increased sensitivity to cell wall stress with the downregulation of chitin synthase-coding genes. These results indicated that the COMPASS core subunits MpSet1 and MpSwd3 help establish H3K4me2/3 for growth and development, spore formation, and pigment synthesis in Monascus. These core subunits also assist in maintaining cell wall integrity.
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Affiliation(s)
- Zhongling Wu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, China
| | - Hongyan Gao
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, China
| | - Zhenmin Liu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, China
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7
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Candela-Ferre J, Diego-Martin B, Pérez-Alemany J, Gallego-Bartolomé J. Mind the gap: Epigenetic regulation of chromatin accessibility in plants. PLANT PHYSIOLOGY 2024; 194:1998-2016. [PMID: 38236303 PMCID: PMC10980423 DOI: 10.1093/plphys/kiae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/23/2023] [Indexed: 01/19/2024]
Abstract
Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins and acting as important signaling hubs. The association of histones with DNA in nucleosomes and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.
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Affiliation(s)
- Joan Candela-Ferre
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
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8
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Zhang B, Wang Z, Dai X, Gao J, Zhao J, Ma R, Chen Y, Sun Y, Ma H, Li S, Zhou C, Wang JP, Li W. A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa. THE NEW PHYTOLOGIST 2024; 241:1950-1972. [PMID: 38095236 DOI: 10.1111/nph.19481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Histone H3 lysine-4 trimethylation (H3K4me3) activating drought-responsive genes in plants for drought adaptation has long been established, but the underlying regulatory mechanisms are unknown. Here, using yeast two-hybrid, bimolecular fluorescence complementation, biochemical analyses, transient and CRISPR-mediated transgenesis in Populus trichocarpa, we unveiled in this adaptation a regulatory interplay between chromatin regulation and gene transactivation mediated by an epigenetic determinant, a PtrSDG2-1-PtrCOMPASS (complex proteins associated with Set1)-like H3K4me3 complex, PtrSDG2-1-PtrWDR5a-1-PtrRbBP5-1-PtrAsh2-2 (PtrSWRA). Under drought conditions, a transcription factor PtrAREB1-2 interacts with PtrSWRA, forming a PtrSWRA-PtrAREB1-2 pentamer, to recruit PtrSWRA to specific promoter elements of drought-tolerant genes, such as PtrHox2, PtrHox46, and PtrHox52, for depositing H3K4me3 to promote and maintain activated state of such genes for tolerance. CRISPR-edited defects in the pentamer impaired drought tolerance and elevated expression of PtrHox2, PtrHox46, or PtrHox52 improved the tolerance as well as growth in P. trichocarpa. Our findings revealed the identity of the underlying H3K4 trimethyltransferase and its interactive arrangement with the COMPASS for catalysis specificity and efficiency. Furthermore, our study uncovered how the H3K4 trimethyltransferase-COMPASS complex is recruited to the effector genes for elevating H3K4me3 marks for improved drought tolerance and growth/biomass production in plants.
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Affiliation(s)
- Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfeng Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Rong Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yanjie Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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9
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Du P, Wang Q, Yuan D, Chen S, Su Y, Li L, Chen S, He X. WRKY transcription factors and OBERON histone-binding proteins form complexes to balance plant growth and stress tolerance. EMBO J 2023; 42:e113639. [PMID: 37565504 PMCID: PMC10548177 DOI: 10.15252/embj.2023113639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023] Open
Abstract
WRKY transcription factors in plants are known to be able to mediate either transcriptional activation or repression, but the mechanism regulating their transcriptional activity is largely unclear. We found that group IId WRKY transcription factors interact with OBERON (OBE) proteins, forming redundant WRKY-OBE complexes in Arabidopsis thaliana. The coiled-coil domain of WRKY transcription factors binds to OBE proteins and is responsible for target gene selection and transcriptional repression. The PHD finger of OBE proteins binds to both histones and WRKY transcription factors. WRKY-OBE complexes repress the transcription of numerous stress-responsive genes and are required for maintaining normal plant growth. Several WRKY and OBE mutants show reduced plant size and increased drought tolerance, accompanied by increased expression of stress-responsive genes. Moreover, expression levels of most of these WRKY and OBE genes are reduced in response to drought stress, revealing a previously uncharacterized regulatory mechanism of the drought stress response. These results suggest that WRKY-OBE complexes repress transcription of stress-responsive genes, and thereby balance plant growth and stress tolerance.
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Affiliation(s)
- Ping Du
- College of Life SciencesBeijing Normal UniversityBeijingChina
- National Institute of Biological SciencesBeijingChina
| | - Qi Wang
- College of Life SciencesBeijing Normal UniversityBeijingChina
- National Institute of Biological SciencesBeijingChina
| | - Dan‐Yang Yuan
- National Institute of Biological SciencesBeijingChina
| | | | - Yin‐Na Su
- National Institute of Biological SciencesBeijingChina
| | - Lin Li
- National Institute of Biological SciencesBeijingChina
| | - She Chen
- National Institute of Biological SciencesBeijingChina
- Tsinghua Institute of Multidisciplinary Biomedical ResearchTsinghua UniversityBeijingChina
| | - Xin‐Jian He
- College of Life SciencesBeijing Normal UniversityBeijingChina
- National Institute of Biological SciencesBeijingChina
- Tsinghua Institute of Multidisciplinary Biomedical ResearchTsinghua UniversityBeijingChina
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10
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Jiang D, Berger F. Variation is important: Warranting chromatin function and dynamics by histone variants. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102408. [PMID: 37399781 DOI: 10.1016/j.pbi.2023.102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
The chromatin of flowering plants exhibits a wide range of sequence variants of the core and linker histones. Recent studies have demonstrated that specific histone variant enrichment, combined with post-translational modifications (PTMs) of histones, defines distinct chromatin states that impact specific chromatin functions. Chromatin remodelers are emerging as key regulators of histone variant dynamics, contributing to shaping chromatin states and regulating gene transcription in response to environment. Recognizing the histone variants by their specific readers, controlled by histone PTMs, is crucial for maintaining genome and chromatin integrity. In addition, various histone variants have been shown to play essential roles in remodeling chromatin domains to facilitate important programmed transitions throughout the plant life cycle. In this review, we discuss recent findings in this exciting field of research, which holds immense promise for many surprising discoveries related to the evolution of complexity in plant organization through a seemingly simple protein family.
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Affiliation(s)
- Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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11
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Liu X, Xing Q, Liu X, Müller-Xing R. Expression of the Populus Orthologues of AtYY1, YIN and YANG Activates the Floral Identity Genes AGAMOUS and SEPALLATA3 Accelerating Floral Transition in Arabidopsis thaliana. Int J Mol Sci 2023; 24:ijms24087639. [PMID: 37108801 PMCID: PMC10146089 DOI: 10.3390/ijms24087639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
YIN YANG 1 (YY1) encodes a dual-function transcription factor, evolutionary conserved between the animal and plant kingdom. In Arabidopsis thaliana, AtYY1 is a negative regulator of ABA responses and floral transition. Here, we report the cloning and functional characterization of the two AtYY1 paralogs, YIN and YANG (also named PtYY1a and PtYY1b) from Populus (Populus trichocarpa). Although the duplication of YY1 occurred early during the evolution of the Salicaceae, YIN and YANG are highly conserved in the willow tree family. In the majority of Populus tissues, YIN was more strongly expressed than YANG. Subcellular analysis showed that YIN-GFP and YANG-GFP are mainly localized in the nuclei of Arabidopsis. Stable and constitutive expression of YIN and YANG resulted in curled leaves and accelerated floral transition of Arabidopsis plants, which was accompanied by high expression of the floral identity genes AGAMOUS (AG) and SEPELLATA3 (SEP3) known to promote leaf curling and early flowering. Furthermore, the expression of YIN and YANG had similar effects as AtYY1 overexpression to seed germination and root growth in Arabidopsis. Our results suggest that YIN and YANG are functional orthologues of the dual-function transcription factor AtYY1 with similar roles in plant development conserved between Arabidopsis and Populus.
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Affiliation(s)
- Xinying Liu
- Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Qian Xing
- Lushan Botanical Garden, Chinese Academy of Sciences (CAS), Jiujiang 332900, China
| | - Xuemei Liu
- Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ralf Müller-Xing
- Lushan Botanical Garden, Chinese Academy of Sciences (CAS), Jiujiang 332900, China
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12
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Zhao F, Xue M, Zhang H, Li H, Zhao T, Jiang D. Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis. THE NEW PHYTOLOGIST 2023; 238:750-764. [PMID: 36647799 DOI: 10.1111/nph.18738] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Plants can sense temperature changes and adjust their development and morphology accordingly in a process called thermomorphogenesis. This phenotypic plasticity implies complex mechanisms regulating gene expression reprogramming in response to environmental alteration. Histone variants often associate with specific chromatin states; yet, how their deposition/eviction modulates transcriptional changes induced by environmental cues remains elusive. In Arabidopsis thaliana, temperature elevation-induced transcriptional activation at thermo-responsive genes entails the chromatin eviction of a histone variant H2A.Z by INO80, which is recruited to these loci via interacting with a key thermomorphogenesis regulator PIF4. Here, we show that both INO80 and the deposition chaperones of another histone variant H3.3 associate with ELF7, a critical component of the transcription elongator PAF1 complex. H3.3 promotes thermomorphogenesis and the high temperature-enhanced RNA Pol II transcription at PIF4 targets, and it is broadly required for the H2A.Z removal-induced gene activation. Reciprocally, INO80 and ELF7 regulate H3.3 deposition, and are necessary for the high temperature-induced H3.3 enrichment at PIF4 targets. Our findings demonstrate close coordination between H2A.Z eviction and H3.3 deposition in gene activation induced by high temperature, and pinpoint the importance of histone variants dynamics in transcriptional regulation.
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Affiliation(s)
- Fengyue Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Mande Xue
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Huairen Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Ting Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
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13
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Xie SS, Zhang YZ, Peng L, Yu DT, Zhu G, Zhao Q, Wang CH, Xie Q, Duan CG. JMJ28 guides sequence-specific targeting of ATX1/2-containing COMPASS-like complex in Arabidopsis. Cell Rep 2023; 42:112163. [PMID: 36827182 DOI: 10.1016/j.celrep.2023.112163] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 09/21/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Despite extensive investigations in mammals and yeasts, the importance and specificity of COMPASS-like complex, which catalyzes histone 3 lysine 4 methylation (H3K4me), are not fully understood in plants. Here, we report that JMJ28, a Jumonji C domain-containing protein in Arabidopsis, recognizes specific DNA motifs through a plant-specific WRC domain and acts as an interacting factor to guide the chromatin targeting of ATX1/2-containing COMPASS-like complex. JMJ28 associates with COMPASS-like complex in vivo via direct interaction with RBL. The DNA-binding activity of JMJ28 is essential for both the targeting specificity of ATX1/2-COMPASS and the deposition of H3K4me at specific loci but exhibit functional redundancy with alternative COMPASS-like complexes at other loci. Finally, we demonstrate that JMJ28 is a negative regulator of plant immunity. In summary, our findings reveal a plant-specific recruitment mechanism of COMPASS-like complex. These findings help to gain deeper insights into the regulatory mechanism of COMPASS-like complex in plants.
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Affiliation(s)
- Si-Si Xie
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Zhe Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ding-Tian Yu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Zhu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qingzhen Zhao
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China
| | - Chun-Han Wang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Ornelas-Ayala D, Cortés-Quiñones C, Olvera-Herrera J, García-Ponce B, Garay-Arroyo A, Álvarez-Buylla ER, Sanchez MDLP. A Green Light to Switch on Genes: Revisiting Trithorax on Plants. PLANTS (BASEL, SWITZERLAND) 2022; 12:75. [PMID: 36616203 PMCID: PMC9824250 DOI: 10.3390/plants12010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
The Trithorax Group (TrxG) is a highly conserved multiprotein activation complex, initially defined by its antagonistic activity with the PcG repressor complex. TrxG regulates transcriptional activation by the deposition of H3K4me3 and H3K36me3 marks. According to the function and evolutionary origin, several proteins have been defined as TrxG in plants; nevertheless, little is known about their interactions and if they can form TrxG complexes. Recent evidence suggests the existence of new TrxG components as well as new interactions of some TrxG complexes that may be acting in specific tissues in plants. In this review, we bring together the latest research on the topic, exploring the interactions and roles of TrxG proteins at different developmental stages, required for the fine-tuned transcriptional activation of genes at the right time and place. Shedding light on the molecular mechanism by which TrxG is recruited and regulates transcription.
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15
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Shang JY, Cai XW, Su YN, Zhang ZC, Wang X, Zhao N, He XJ. Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2438-2454. [PMID: 36354145 DOI: 10.1111/jipb.13406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Although the Trithorax histone methyltransferases ATX1-5 are known to regulate development and stress responses by catalyzing histone H3K4 methylation in Arabidopsis thaliana, it is unknown whether and how these histone methyltransferases affect DNA methylation. Here, we found that the redundant ATX1-5 proteins are not only required for plant development and viability but also for the regulation of DNA methylation. The expression and H3K4me3 levels of both RNA-directed DNA methylation (RdDM) genes (NRPE1, DCL3, IDN2, and IDP2) and active DNA demethylation genes (ROS1, DML2, and DML3) were downregulated in the atx1/2/4/5 mutant. Consistent with the facts that the active DNA demethylation pathway mediates DNA demethylation mainly at CG and CHG sites, and that the RdDM pathway mediates DNA methylation mainly at CHH sites, whole-genome DNA methylation analyses showed that hyper-CG and CHG DMRs in atx1/2/4/5 significantly overlapped with those in the DNA demethylation pathway mutant ros1 dml2 dml3 (rdd), and that hypo-CHH DMRs in atx1/2/4/5 significantly overlapped with those in the RdDM mutant nrpe1, suggesting that the ATX paralogues function redundantly to regulate DNA methylation by promoting H3K4me3 levels and expression levels of both RdDM genes and active DNA demethylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex components function as a whole to regulate DNA methylation. This study reveals a previously uncharacterized mechanism underlying the regulation of DNA methylation.
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Affiliation(s)
- Ji-Yun Shang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Chen Zhang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin Wang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Nan Zhao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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16
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Guo J, Cai G, Li YQ, Zhang YX, Su YN, Yuan DY, Zhang ZC, Liu ZZ, Cai XW, Guo J, Li L, Chen S, He XJ. Comprehensive characterization of three classes of Arabidopsis SWI/SNF chromatin remodelling complexes. NATURE PLANTS 2022; 8:1423-1439. [PMID: 36471048 DOI: 10.1038/s41477-022-01282-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
Although SWI/SNF chromatin remodelling complexes are known to regulate diverse biological functions in plants, the classification, compositions and functional mechanisms of the complexes remain to be determined. Here we comprehensively characterized SWI/SNF complexes by affinity purification and mass spectrometry in Arabidopsis thaliana, and found three classes of SWI/SNF complexes, which we termed BAS, SAS and MAS (BRM-, SYD- and MINU1/2-associated SWI/SNF complexes). By investigating multiple developmental phenotypes of SWI/SNF mutants, we found that three classes of SWI/SNF complexes have both overlapping and specific functions in regulating development. To investigate how the three classes of SWI/SNF complexes differentially regulate development, we mapped different SWI/SNF components on chromatin at the whole-genome level and determined their effects on chromatin accessibility. While all three classes of SWI/SNF complexes regulate chromatin accessibility at proximal promoter regions, SAS is a major SWI/SNF complex that is responsible for mediating chromatin accessibility at distal promoter regions and intergenic regions. Histone modifications are related to both the association of SWI/SNF complexes with chromatin and the SWI/SNF-dependent chromatin accessibility. Three classes of SWI/SNF-dependent accessibility may enable different sets of transcription factors to access chromatin. These findings lay a foundation for further investigation of the function of three classes of SWI/SNF complexes in plants.
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Affiliation(s)
- Jing Guo
- College of Life Sciences, Beijing Normal University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Guang Cai
- National Institute of Biological Sciences, Beijing, China
| | - Yong-Qiang Li
- National Institute of Biological Sciences, Beijing, China
| | - Yi-Xuan Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, China
| | - Dan-Yang Yuan
- National Institute of Biological Sciences, Beijing, China
| | | | - Zhen-Zhen Liu
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, China
| | - Jing Guo
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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17
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Hu H, Du J. Structure and mechanism of histone methylation dynamics in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102211. [PMID: 35452951 DOI: 10.1016/j.pbi.2022.102211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Histone methylation plays a central role in regulating chromatin state and gene expression in Arabidopsis and is involved in a variety of physiological and developmental processes. Dynamic regulation of histone methylation relies on both histone methyltransferase "writer" and histone demethylases "eraser" proteins. In this review, we focus on the four major histone methylation modifications in Arabidopsis H3, H3K4, H3K9, H3K27, and H3K36, and summarize current knowledge of the dynamic regulation of these modifications, with an emphasis on the biochemical and structural perspectives of histone methyltransferases and demethylases.
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Affiliation(s)
- Hongmiao Hu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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18
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Zhao G, Wang J, Chen X, Sha H, Liu X, Han Y, Qiu G, Zhang F, Fang J. OsASHL1 and OsASHL2, two members of the COMPASS-like complex, control floral transition and plant development in rice. J Genet Genomics 2022; 49:870-880. [DOI: 10.1016/j.jgg.2022.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 11/26/2022]
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19
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Sureshkumar S, Balasubramanian S. Complexes and complexities: INO80 takes center stage. MOLECULAR PLANT 2021; 14:1776-1778. [PMID: 34418552 DOI: 10.1016/j.molp.2021.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
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20
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Osnato M. A COMPASS to guide vegetative growth and the floral transition. THE PLANT CELL 2021; 33:3179-3180. [PMID: 35233593 PMCID: PMC8505863 DOI: 10.1093/plcell/koab191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Michela Osnato
- Assistant Features Editor, The Plant Cell
- Institute de Ciencia i Tecnologia Ambientals, Universitat Aut�noma de Barcelona (ICTA-UAB)
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