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Haider S, Farrona S. Decoding histone 3 lysine methylation: Insights into seed germination and flowering. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102598. [PMID: 38986392 DOI: 10.1016/j.pbi.2024.102598] [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: 04/01/2024] [Revised: 06/01/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
Histone lysine methylation is a highly conserved epigenetic modification across eukaryotes that contributes to creating different dynamic chromatin states, which may result in transcriptional changes. Over the years, an accumulated set of evidence has shown that histone methylation allows plants to align their development with their surroundings, enabling them to respond and memorize past events due to changes in the environment. In this review, we discuss the molecular mechanisms of histone methylation in plants. Writers, readers, and erasers of Arabidopsis histone methylation marks are described with an emphasis on their role in two of the most important developmental transition phases in plants, seed germination and flowering. Further, the crosstalk between different methylation marks is also discussed. An overview of the mechanisms of histone methylation modifications and their biological outcomes will shed light on existing research gaps and may provide novel perspectives to increase crop yield and resistance in the era of global climate change.
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Affiliation(s)
- Saqlain Haider
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland.
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2
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Liu N, Hu Z, Zhang L, Yang Q, Deng L, Terzaghi W, Hua W, Yan M, Liu J, Zheng M. BAPID suppresses the inhibition of BRM on Di19-PR module in response to drought. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:253-271. [PMID: 39166483 DOI: 10.1111/tpj.16984] [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: 03/29/2024] [Revised: 07/26/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Drought is one of the most important abiotic stresses, and seriously threatens plant development and productivity. Increasing evidence indicates that chromatin remodelers are pivotal for plant drought response. However, molecular mechanisms of chromatin remodelers-mediated plant drought responses remain obscure. In this study, we found a novel interactor of BRM called BRM-associated protein involved in drought response (BAPID), which interacted with SWI/SNF chromatin remodeler BRM and drought-induced transcription factor Di19. Our findings demonstrated that BAPID acted as a positive drought regulator since drought tolerance was increased in BAPID-overexpressing plants, but decreased in BAPID-deficient plants, and physically bound to PR1, PR2, and PR5 promoters to mediate expression of PR genes to defend against dehydration stress. Genetic approaches demonstrated that BRM acted epistatically to BAPID and Di19 in drought response in Arabidopsis. Furthermore, the BAPID protein-inhibited interaction between BRM and Di19, and suppressed the inhibition of BRM on the Di19-PR module by mediating the H3K27me3 deposition at PR loci, thus changing nucleosome accessibility of Di19 and activating transcription of PR genes in response to drought. Our results shed light on the molecular mechanism whereby the BAPID-BRM-Di19-PRs pathway mediates plant drought responses. We provide data improving our understanding of chromatin remodeler-mediated plant drought regulation network.
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Affiliation(s)
- Nian Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Zhiyong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Liang Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Qian Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Yuelushan Laboratory, Changsha, 410125, China
| | - Linbin Deng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, USA
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Yuelushan Laboratory, Changsha, 410125, China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
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Liang Z, Zhu T, Yu Y, Wu C, Huang Y, Hao Y, Song X, Fu W, Yuan L, Cui Y, Huang S, Li C. PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation. Mol Cell 2024; 84:3438-3454.e8. [PMID: 39232583 DOI: 10.1016/j.molcel.2024.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 06/19/2024] [Accepted: 08/12/2024] [Indexed: 09/06/2024]
Abstract
Spreading of H3K27me3 is crucial for the maintenance of mitotically inheritable Polycomb-mediated chromatin silencing in animals and plants. However, how Polycomb repressive complex 2 (PRC2) accesses unmodified nucleosomes in spreading regions for spreading H3K27me3 remains unclear. Here, we show in Arabidopsis thaliana that the chromatin remodeler PICKLE (PKL) plays a specialized role in H3K27me3 spreading to safeguard cell identity during differentiation. PKL specifically localizes to H3K27me3 spreading regions but not to nucleation sites and physically associates with PRC2. Loss of PKL disrupts the occupancy of the PRC2 catalytic subunit CLF in spreading regions and leads to aberrant dedifferentiation. Nucleosome density increase endowed by the ATPase function of PKL ensures that unmodified nucleosomes are accessible to PRC2 catalytic activity for H3K27me3 spreading. Our findings demonstrate that PKL-dependent nucleosome compaction is critical for PRC2-mediated H3K27me3 read-and-write function in H3K27me3 spreading, thus revealing a mechanism by which repressive chromatin domains are established and propagated.
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Affiliation(s)
- Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Caihong Wu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yisui Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuanhao Hao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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Zhang C, Xiong AT, Ren MY, Zhao YY, Huang MJ, Huang LC, Zhang Z, Wang Y, Zheng QQ, Fan J, Guan JJ, Yang ZN. An epigenetically mediated double negative cascade from EFD to HB21 regulates anther development. Nat Commun 2024; 15:7796. [PMID: 39242635 PMCID: PMC11379828 DOI: 10.1038/s41467-024-52114-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
Epigenetic modifications are crucial for plant development. EFD (Exine Formation Defect) encodes a SAM-dependent methyltransferase that is essential for the pollen wall pattern formation and male fertility in Arabidopsis. In this study, we find that the expression of DRM2, a de novo DNA methyltransferase in plants, complements for the defects in efd, suggesting its potential de novo DNA methyltransferase activity. Genetic analysis indicates that EFD functions through HB21, as the knockout of HB21 fully restores fertility in efd mutants. DNA methylation and histone modification analyses reveal that EFD represses the transcription of HB21 through epigenetic mechanisms. Additionally, we demonstrate that HB21 directly represses the expression of genes crucial for pollen formation and anther dehiscence, including CalS5, RPG1/SWEET8, CYP703A2 and NST2. Collectively, our findings unveil a double negative regulatory cascade mediated by epigenetic modifications that coordinates anther development, offering insights into the epigenetic regulation of this process.
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Affiliation(s)
- Cheng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ao-Tong Xiong
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Meng-Yi Ren
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yan-Yun Zhao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Min-Jia Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Long-Cheng Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zheng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yun Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Quan-Quan Zheng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jing Fan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jing-Jing Guan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhong-Nan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
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5
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Go D, Lu B, Alizadeh M, Gazzarrini S, Song L. Voice from both sides: a molecular dialogue between transcriptional activators and repressors in seed-to-seedling transition and crop adaptation. FRONTIERS IN PLANT SCIENCE 2024; 15:1416216. [PMID: 39166233 PMCID: PMC11333834 DOI: 10.3389/fpls.2024.1416216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/20/2024] [Indexed: 08/22/2024]
Abstract
High-quality seeds provide valuable nutrients to human society and ensure successful seedling establishment. During maturation, seeds accumulate storage compounds that are required to sustain seedling growth during germination. This review focuses on the epigenetic repression of the embryonic and seed maturation programs in seedlings. We begin with an extensive overview of mutants affecting these processes, illustrating the roles of core proteins and accessory components in the epigenetic machinery by comparing mutants at both phenotypic and molecular levels. We highlight how omics assays help uncover target-specific functional specialization and coordination among various epigenetic mechanisms. Furthermore, we provide an in-depth discussion on the Seed dormancy 4 (Sdr4) transcriptional corepressor family, comparing and contrasting their regulation of seed germination in the dicotyledonous species Arabidopsis and two monocotyledonous crops, rice and wheat. Finally, we compare the similarities in the activation and repression of the embryonic and seed maturation programs through a shared set of cis-regulatory elements and discuss the challenges in applying knowledge largely gained in model species to crops.
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Affiliation(s)
- Dongeun Go
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Bailan Lu
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Sonia Gazzarrini
- Department of Biological Science, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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6
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Li Z, Zeng J, Zhou Y, Ding X, Jiang G, Wu K, Jiang Y, Duan X. Histone H3K27 demethylase SlJMJ3 modulates fruit ripening in tomato. PLANT PHYSIOLOGY 2024; 195:2727-2742. [PMID: 38669310 DOI: 10.1093/plphys/kiae233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 02/12/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The histone lysine (K) demethylase 4 (KDM4/JHDM3) subfamily of jumonji domain-containing demethylases (JMJs) has been implicated in various aspects of plant development. However, their involvement in regulating the ripening of fleshy fruits remains unclear. In this study, we identified SlJMJ3, a member of the KDM4/JHDM3 family, as an H3K27me3 demethylase in tomato (Solanum lycopersicum) that plays an important role in fruit ripening regulation. Overexpression of SlJMJ3 leads to accelerated fruit ripening, whereas loss of function of SlJMJ3 delays this process. Furthermore, we determined that SlJMJ3 exerts its regulatory function by modulating the expression of multiple ripening-related genes involved in ethylene biosynthesis and response, carotenoid metabolism, cell wall modification, transcriptional control, and DNA methylation modification. SlJMJ3 binds directly to the promoters of ripening-related genes harboring the CTCTGYTY motif and activates their expression. Additionally, SlJMJ3 reduces the levels of H3K27me3 at its target genes, thereby upregulating their expression. In summary, our findings highlight the role of SlJMJ3 in the regulation of fruit ripening in tomato. By removing the methyl group from trimethylated histone H3 lysine 27 at ripening-related genes, SlJMJ3 acts as an epigenetic regulator that orchestrates the complex molecular processes underlying fruit ripening.
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Affiliation(s)
- Zhiwei Li
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijie Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Guangdong AIB Polytechnic, Guangzhou 510507, China
| | - Xiaochun Ding
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Guoxiang Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Yueming Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xuewu Duan
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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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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Menon G, Mateo-Bonmati E, Reeck S, Maple R, Wu Z, Ietswaart R, Dean C, Howard M. Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing. Mol Cell 2024; 84:2255-2271.e9. [PMID: 38851186 DOI: 10.1016/j.molcel.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 02/28/2024] [Accepted: 05/14/2024] [Indexed: 06/10/2024]
Abstract
The mechanisms and timescales controlling de novo establishment of chromatin-mediated transcriptional silencing by Polycomb repressive complex 2 (PRC2) are unclear. Here, we investigate PRC2 silencing at Arabidopsis FLOWERING LOCUS C (FLC), known to involve co-transcriptional RNA processing, histone demethylation activity, and PRC2 function, but so far not mechanistically connected. We develop and test a computational model describing proximal polyadenylation/termination mediated by the RNA-binding protein FCA that induces H3K4me1 removal by the histone demethylase FLD. H3K4me1 removal feeds back to reduce RNA polymerase II (RNA Pol II) processivity and thus enhance early termination, thereby repressing productive transcription. The model predicts that this transcription-coupled repression controls the level of transcriptional antagonism to PRC2 action. Thus, the effectiveness of this repression dictates the timescale for establishment of PRC2/H3K27me3 silencing. We experimentally validate these mechanistic model predictions, revealing that co-transcriptional processing sets the level of productive transcription at the locus, which then determines the rate of the ON-to-OFF switch to PRC2 silencing.
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Affiliation(s)
- Govind Menon
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Eduardo Mateo-Bonmati
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhe Wu
- 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, China
| | - Robert Ietswaart
- Harvard Medical School, Department of Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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Poza-Viejo L, Payá-Milans M, Wilkinson MD, Piñeiro M, Jarillo JA, Crevillén P. Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time. PLANTA 2024; 260:27. [PMID: 38865018 PMCID: PMC11169032 DOI: 10.1007/s00425-024-04454-7] [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: 01/15/2024] [Accepted: 06/02/2024] [Indexed: 06/13/2024]
Abstract
MAIN CONCLUSION In Brassica rapa, the epigenetic modifier BraA.CLF orchestrates flowering by modulating H3K27me3 levels at the floral integrator genes FT, SOC1, and SEP3, thereby influencing their expression. CURLY LEAF (CLF) is the catalytic subunit of the plant Polycomb Repressive Complex 2 that mediates the trimethylation of histone H3 lysine 27 (H3K27me3), an epigenetic modification that leads to gene silencing. While the function of CURLY LEAF (CLF) has been extensively studied in Arabidopsis thaliana, its role in Brassica crops is barely known. In this study, we focused on the Brassica rapa homolog of CLF and found that the loss-of-function mutant braA.clf-1 exhibits an accelerated flowering together with pleiotropic phenotypic alterations compared to wild-type plants. In addition, we carried out transcriptomic and H3K27me3 genome-wide analyses to identify the genes regulated by BraA.CLF. Interestingly, we observed that several floral regulatory genes, including the B. rapa homologs of FT, SOC1 and SEP3, show reduced H3K27me3 levels and increased transcript levels compared to wild-type plants, suggesting that they are direct targets of BraA.CLF and key players in regulating flowering time in this crop. In addition, the results obtained will enhance our understanding of the epigenetic mechanisms regulating key developmental traits and will aid to increase crop yield by engineering new Brassica varieties with different flowering time requirements.
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Affiliation(s)
- Laura Poza-Viejo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Miriam Payá-Milans
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Seville, Spain
| | - Mark D Wilkinson
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain.
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10
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Gómez-Martínez D, Barrero-Gil J, Tranque E, Ruiz MF, Catalá R, Salinas J. SVALKA-POLYCOMB REPRESSIVE COMPLEX2 module controls C-REPEAT BINDING FACTOR3 induction during cold acclimation. PLANT PHYSIOLOGY 2024; 195:1152-1160. [PMID: 38124468 PMCID: PMC11142377 DOI: 10.1093/plphys/kiad671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
C-REPEAT BINDING FACTORS (CBFs) are highly conserved plant transcription factors that promote cold tolerance. In Arabidopsis (Arabidopsis thaliana), three CBFs (CBF1 to CBF3) play a critical role in cold acclimation, and the expression of their corresponding genes is rapidly and transiently induced during this adaptive response. Cold induction of CBFs has been extensively studied and shown to be tightly controlled, yet the molecular mechanisms that restrict the expression of each CBF after their induction during cold acclimation are poorly understood. Here, we present genetic and molecular evidence that the decline in the induction of CBF3 during cold acclimation is epigenetically regulated through the Polycomb Repressive Complex (PRC) 2. We show that this complex promotes the deposition of the repressive mark H3K27me3 at the coding region of CBF3, silencing its expression. Our results indicate that the cold-inducible long noncoding RNA SVALKA is essential for this regulation by recruiting PRC2 to CBF3. These findings unveil a SVALKA-PRC2 regulatory module that ensures the precise timing of CBF3 induction during cold acclimation and the correct development of this adaptive response.
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Affiliation(s)
- Diego Gómez-Martínez
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Javier Barrero-Gil
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Eduardo Tranque
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Fernanda Ruiz
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Rafael Catalá
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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11
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Wang H, Yin C, Zhang G, Yang M, Zhu B, Jiang J, Zeng Z. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modification and nucleosome depletion in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:549-564. [PMID: 38184780 DOI: 10.1111/tpj.16624] [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: 05/14/2022] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Epigenetic regulation of gene expression plays a crucial role in plant development and environmental adaptation. The H3K4me3 and H3K27me3 have not only been discovered in the regulation of gene expression in multiple biological processes but also in responses to abiotic stresses in plants. However, evidence for the presence of both H3K4me3 and H3K27me3 on the same nucleosome is sporadic. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modifications and nucleosome depletion over a considerable number of active genes is documented in potato tubers and provides clues on an additional role of the bivalent modifications. Limited by the available information of genes encoding PcG/TrxG proteins as well as their corresponding mutants in potatoes, the molecular mechanism underlying the cold-induced deposition of the bivalent mark remains elusive. In this study, we found a similar deposition of the bivalent H3K4me3-H3K27me3 mark over 2129 active genes in cold-treated Arabidopsis Col-0 seedlings. The expression levels of the bivalent mark-associated genes tend to be independent of bivalent modification levels. However, these genes were associated with greater chromatin accessibility, presumably to provide a distinct chromatin environment for gene expression. In mutants clf28 and lhp1, failure to deposit H3K27me3 in active genes upon cold treatment implies that the CLF is potentially involved in cold-induced deposition of H3K27me3, with assistance from LHP1. Failure to deposit H3K4me3 during cold treatment in atx1-2 suggests a regulatory role of ATX1 in the deposition of H3K4me3. In addition, we observed a cold-induced global reduction in nucleosome occupancy, which is potentially mediated by LHP1 in an H3K27me3-dependent manner.
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Affiliation(s)
- Hao Wang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Chang Yin
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Guoyan Zhang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Miao Yang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University AgBioResearch, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Zixian Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, 610101, Sichuan, China
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12
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Čermák V, Kašpar T, Fischer L. SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway. FRONTIERS IN PLANT SCIENCE 2024; 15:1372880. [PMID: 38576781 PMCID: PMC10991848 DOI: 10.3389/fpls.2024.1372880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
RNA-directed DNA methylation (RdDM) is driven by small RNAs (sRNAs) complementary to the nascent transcript of RNA polymerase V (Pol V). sRNAs associated with ARGONAUTE (AGO) proteins are tethered to Pol V mainly by the AGO-hook domain of its subunit NRPE1. We found, by in silico analyses, that Pol V strongly colocalizes on chromatin with another AGO-hook protein, SPT6-like (SPT6L), which is a known essential transcription elongation factor of Pol II. Our phylogenetic analysis revealed that SPT6L acquired its AGO-binding capacity already in the most basal streptophyte algae, even before the emergence of Pol V, suggesting that SPT6L might be a driving force behind the RdDM evolution. Since its emergence, SPT6L with the AGO-hook represents the only conserved SPT6 homolog in Viridiplantae, implying that the same protein is involved in both Pol II and Pol V complexes. To better understand the role of SPT6L in the Pol V complex, we characterized genomic loci where these two colocalize and uncovered that DNA methylation there is more dynamic, driven by higher levels of sRNAs often from non-canonical RdDM pathways and more dependent on chromatin modifying and remodeling proteins like MORC. Pol V loci with SPT6L are highly depleted in helitrons but enriched in gene promoters for which locally and temporally precise methylation is necessary. In view of these results, we discuss potential roles of multiple AGO-hook domains present in the Pol V complex and speculate that SPT6L mediates de novo methylation of naïve loci by interconnecting Pol II and Pol V activities.
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Affiliation(s)
- Vojtěch Čermák
- Laboratory of Plant Cell Biology and Biotechnology, Faculty of Science, Department of Experimental Plant Biology, Charles University, Prague, Czechia
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13
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Ornelas-Ayala D, Cortés-Quiñones C, Arciniega-González JA, Garay-Arroyo A, García-Ponce B, R Alvarez-Buylla E, Sanchez MDLP. ULTRAPETALAs in action: Unraveling their role in root development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111975. [PMID: 38181854 DOI: 10.1016/j.plantsci.2024.111975] [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: 09/21/2023] [Revised: 12/19/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
The epigenetic complex Trithorax (TrxG) regulates gene transcription through post-translational histone modifications and is involved in a wide range of developmental processes. ULTRAPETALA1 (ULT1) is a SAND domain plant-exclusive TrxG protein that regulates the H3K4me3 active mark to counteract PcG repression. ULT1 has been identified to be involved in multiple tissue-specific processes. In the Arabidopsis root, ULT1 is required to maintain the stem cell niche, a role that is independent of the histone methyltransferase ATX1. Here we show the contribution of ULT2 in the maintenance of root stem cell niche. We also analyzed the gene expression in the ult1, ult2, and ult1ult2 mutants, evidencing three ways in which ULT1 and ULT2 regulate gene expression, one of them, where ULT1 or ULT2 regulate specific genes each, another where ULT1 and ULT2 act redundantly, as well as a regulation that requires of ULT1 and ULT2 together, supporting a coregulation, never reported. Furthermore, we also evidenced the participation of ULT1 in transcriptional repression synergically with CLF, a key histone methyltransferase of PcG.
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Affiliation(s)
- Diego Ornelas-Ayala
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, Mexico.
| | - Carlos Cortés-Quiñones
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, Mexico.
| | - J Arturo Arciniega-González
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, Mexico.
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, Mexico.
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, Mexico.
| | - Elena R Alvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, Mexico.
| | - Maria De La Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, Mexico.
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14
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Godwin J, Govindasamy M, Nedounsejian K, March E, Halton R, Bourbousse C, Wolff L, Fort A, Krzyszton M, López Corrales J, Swiezewski S, Barneche F, Schubert D, Farrona S. The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development. Nat Commun 2024; 15:667. [PMID: 38253560 PMCID: PMC10803359 DOI: 10.1038/s41467-023-44546-8] [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: 11/15/2022] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs' interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs' epigenetic hallmarks in Arabidopsis thaliana. We demonstrated that UBP5 is a plant developmental regulator based on functional analyses of ubp5-CRISPR Cas9 mutant plants. UBP5 promotes H2A monoubiquitination erasure, leading to transcriptional de-repression. Furthermore, preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, acting as an antagonist of the pivotal epigenetic repressive marks H2Aub and H3K27me3, UBP5 provides novel insights to disentangle the complex regulation of PRCs' activities.
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Affiliation(s)
- James Godwin
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Mohan Govindasamy
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Kiruba Nedounsejian
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Eduardo March
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Ronan Halton
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Antoine Fort
- Dept. of Veterinary and Microbial Sciences, Technological University of The Shannon: Midlands, Athlone, Co., Roscommon, Ireland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Jesús López Corrales
- Molecular Parasitology Laboratory (MPL), Centre for One Health and Ryan Institute, School of Natural Sciences, University of Galway, Galway, H91 DK59, Ireland
| | - Szymon Swiezewski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland.
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15
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Franco-Echevarría E, Nielsen M, Schulten A, Cheema J, Morgan TE, Bienz M, Dean C. Distinct accessory roles of Arabidopsis VEL proteins in Polycomb silencing. Genes Dev 2023; 37:801-817. [PMID: 37734835 PMCID: PMC7615239 DOI: 10.1101/gad.350814.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023]
Abstract
Polycomb repressive complex 2 (PRC2) mediates epigenetic silencing of target genes in animals and plants. In Arabidopsis, PRC2 is required for the cold-induced epigenetic silencing of the FLC floral repressor locus to align flowering with spring. During this process, PRC2 relies on VEL accessory factors, including the constitutively expressed VRN5 and the cold-induced VIN3. The VEL proteins are physically associated with PRC2, but their individual functions remain unclear. Here, we show an intimate association between recombinant VRN5 and multiple components within a reconstituted PRC2, dependent on a compact conformation of VRN5 central domains. Key residues mediating this compact conformation are conserved among VRN5 orthologs across the plant kingdom. In contrast, VIN3 interacts with VAL1, a transcriptional repressor that binds directly to FLC These associations differentially affect their role in H3K27me deposition: Both proteins are required for H3K27me3, but only VRN5 is necessary for H3K27me2. Although originally defined as vernalization regulators, VIN3 and VRN5 coassociate with many targets in the Arabidopsis genome that are modified with H3K27me3. Our work therefore reveals the distinct accessory roles for VEL proteins in conferring cold-induced silencing on FLC, with broad relevance for PRC2 targets generally.
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Affiliation(s)
- Elsa Franco-Echevarría
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Mathias Nielsen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Anna Schulten
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Tomos E Morgan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Mariann Bienz
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Caroline Dean
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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16
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Sun L, Cao Y, Li Z, Liu Y, Yin X, Deng XW, He H, Qian W. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1966-1982. [PMID: 37154484 DOI: 10.1111/jipb.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
Abstract
Higher-order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome. We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG-medicated chromatin loops are stable, many of these loops are tissue-specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max, indicating that these long-range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.
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Affiliation(s)
- Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Yuxin Cao
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yi Liu
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xiaochang Yin
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
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17
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Antoniou-Kourounioti RL, Meschichi A, Reeck S, Berry S, Menon G, Zhao Y, Fozard J, Holmes T, Zhao L, Wang H, Hartley M, Dean C, Rosa S, Howard M. Integrating analog and digital modes of gene expression at Arabidopsis FLC. eLife 2023; 12:e79743. [PMID: 37466633 DOI: 10.7554/elife.79743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/25/2023] [Indexed: 07/20/2023] Open
Abstract
Quantitative gene regulation at the cell population level can be achieved by two fundamentally different modes of regulation at individual gene copies. A 'digital' mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an 'analog' mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), 'digital' Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modeling, we find that FLC expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at the cell population level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.
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Affiliation(s)
- Rea L Antoniou-Kourounioti
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anis Meschichi
- Swedish University of Agricultural Sciences, Plant Biology Department, Uppsala, Sweden
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Govind Menon
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Yusheng Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - John Fozard
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Terri Holmes
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Lihua Zhao
- Swedish University of Agricultural Sciences, Plant Biology Department, Uppsala, Sweden
| | - Huamei Wang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Matthew Hartley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Plant Biology Department, Uppsala, Sweden
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
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18
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Fal K, Berr A, Le Masson M, Faigenboim A, Pano E, Ishkhneli N, Moyal NL, Villette C, Tomkova D, Chabouté ME, Williams LE, Carles CC. Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis. THE NEW PHYTOLOGIST 2023; 238:1085-1100. [PMID: 36779574 DOI: 10.1111/nph.18666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/28/2022] [Indexed: 06/18/2023]
Abstract
Chromatin is a dynamic platform within which gene expression is controlled by epigenetic modifications, notably targeting amino acid residues of histone H3. Among them is lysine 27 of H3 (H3K27), the trimethylation of which by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatiotemporal patterns of key developmental genes. H3K27 is also subjected to acetylation and is found at sites of active transcription. Most information on the function of histone residues and their associated modifications in plants was obtained from studies of loss-of-function mutants for the complexes that modify them. To decrypt the genuine function of H3K27, we expressed a non-modifiable variant of H3 at residue K27 (H3.3K27A ) in Arabidopsis, and developed a multi-scale approach combining in-depth phenotypical and cytological analyses, with transcriptomics and metabolomics. We uncovered that the H3.3K27A variant causes severe developmental defects, part of them are reminiscent of PRC2 mutants, part of them are new. They include early flowering, increased callus formation and short stems with thicker xylem cell layer. This latest phenotype correlates with mis-regulation of phenylpropanoid biosynthesis. Overall, our results reveal novel roles of H3K27 in plant cell fates and metabolic pathways, and highlight an epigenetic control point for elongation and lignin composition of the stem.
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Affiliation(s)
- Kateryna Fal
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Marie Le Masson
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Adi Faigenboim
- Institute of Plant Sciences, ARO Volcani Center, PO Box 15159, Rishon LeZion, 7528809, Israel
| | - Emeline Pano
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Nickolay Ishkhneli
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Netta-Lee Moyal
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Leor Eshed Williams
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Cristel C Carles
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
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19
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Kim J, Bordiya Y, Xi Y, Zhao B, Kim DH, Pyo Y, Zong W, Ricci WA, Sung S. Warm temperature-triggered developmental reprogramming requires VIL1-mediated, genome-wide H3K27me3 accumulation in Arabidopsis. Development 2023; 150:dev201343. [PMID: 36762655 PMCID: PMC10110417 DOI: 10.1242/dev.201343] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Changes in ambient temperature immensely affect developmental programs in many species. Plants adapt to high ambient growth temperature in part by vegetative and reproductive developmental reprogramming, known as thermo-morphogenesis. Thermo-morphogenesis is accompanied by massive changes in the transcriptome upon temperature change. Here, we show that transcriptome changes induced by warm ambient temperature require VERNALIZATION INSENSITIVE 3-LIKE 1 (VIL1), a facultative component of the Polycomb repressive complex PRC2, in Arabidopsis. Warm growth temperature elicits genome-wide accumulation of H3K27me3 and VIL1 is necessary for the warm temperature-mediated accumulation of H3K27me3. Consistent with its role as a mediator of thermo-morphogenesis, loss of function of VIL1 results in hypo-responsiveness to warm ambient temperature. Our results show that VIL1 is a major chromatin regulator in responses to high ambient temperature.
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Affiliation(s)
- Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yogendra Bordiya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yanpeng Xi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dong-Hwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Youngjae Pyo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - William A. Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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20
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Nugroho ABD, Kim S, Lee SW, Kim DH. Transcriptomic and epigenomic analyses revealed that polycomb repressive complex 2 regulates not only developmental but also stress responsive metabolism in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2023; 14:1079218. [PMID: 36890886 PMCID: PMC9986605 DOI: 10.3389/fpls.2023.1079218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Polycomb group proteins (PcG) play a crucial role in developmental programs in eukaryotic organisms, including plants. PcG-mediated gene repression is achieved by epigenetic histone modification on target chromatins. Loss of PcG components leads to severe developmental defects. CURLY LEAF (CLF), a PcG component in Arabidopsis, catalyzes the trimethylation of histone H3 on lysine 27 (H3K27me3), a repressive histone mark in numerous genes in Arabidopsis. In this study, we isolated a single homolog of Arabidopsis CLF, namely, BrCLF, in Brassica rapa ssp. trilocularis. Transcriptomic analysis revealed that BrCLF participated in B. rapa developmental processes, such as seed dormancy, leaf and flower organ development, and floral transition. BrCLF was also involved in stress signaling and stress-responsive metabolism, such as aliphatic and indolic glucosinolate metabolism in B. rapa. Epigenome analysis showed that H3K27me3 was substantially enriched in genes related to these developmental and stress-responsive processes. Thus, this study provided a basis for elucidating the molecular mechanism of the PcG-mediated regulation of development and stress responses in B. rapa.
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21
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Yu Y, Wang Y, Yao Z, Wang Z, Xia Z, Lee J. Comprehensive Survey of ChIP-Seq Datasets to Identify Candidate Iron Homeostasis Genes Regulated by Chromatin Modifications. Methods Mol Biol 2023; 2665:95-111. [PMID: 37166596 DOI: 10.1007/978-1-0716-3183-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Vital biochemical reactions including photosynthesis to respiration require iron, which should be tightly regulated. Although increasing evidence reveals the importance of epigenetic regulation in gene expression and signaling, the role of histone modifications and chromatin remodeling in plant iron homeostasis is not well understood. In this study, we surveyed publicly available ChIP-seq datasets of Arabidopsis wild-type and mutants defective in key enzymes of histone modification and chromatin remodeling and compared the deposition of epigenetic marks on loci of genes involved in iron regulation. Based on the analysis, we compiled a comprehensive list of iron homeostasis genes with differential enrichment of various histone modifications. This report will provide a resource for future studies to investigate epigenetic regulatory mechanisms of iron homeostasis in plants.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Yuxin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Zhujun Yao
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Zijun Xia
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China.
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22
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Shu J, Ding N, Liu J, Cui Y, Chen C. Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis. Nucleic Acids Res 2022; 50:12754-12767. [PMID: 36453990 PMCID: PMC9825159 DOI: 10.1093/nar/gkac1126] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/10/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be restored mainly by SPT6LΔtSH2, which binds to TSS in a RNA polymerase II (Pol II)-independent manner. Furthermore, SPT6L and SYD/BRM are involved in regulating the nucleosome and Pol II occupancy around TSS. The presence of SPT6L is sufficient to restore the association of the chromatin remodeler SYD to chromatin and maintain normal nucleosome occupancy. Our findings suggest that the two chromatin remodelers can form protein complexes with the core subunit of the transcription machinery and regulate nucleosome occupancy in the early transcription stage.
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Affiliation(s)
- Jie Shu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Ning Ding
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Chen Chen
- To whom correspondence should be addressed. Tel: +86 20 37252711;
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23
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Kim ED, Dorrity MW, Fitzgerald BA, Seo H, Sepuru KM, Queitsch C, Mitsuda N, Han SK, Torii KU. Dynamic chromatin accessibility deploys heterotypic cis/trans-acting factors driving stomatal cell-fate commitment. NATURE PLANTS 2022; 8:1453-1466. [PMID: 36522450 PMCID: PMC9788986 DOI: 10.1038/s41477-022-01304-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/28/2022] [Indexed: 05/12/2023]
Abstract
Chromatin architecture and transcription factor (TF) binding underpin cell-fate specification during development, but their mutual regulatory relationships remain unclear. Here we report an atlas of dynamic chromatin landscapes during stomatal cell-lineage progression, in which sequential cell-state transitions are governed by lineage-specific bHLH TFs. Major reprogramming of chromatin accessibility occurs at the proliferation-to-differentiation transition. We discover novel co-cis regulatory elements (CREs) signifying the early precursor stage, BBR/BPC (GAGA) and bHLH (E-box) motifs, where master-regulatory bHLH TFs, SPEECHLESS and MUTE, consecutively bind to initiate and terminate the proliferative state, respectively. BPC TFs complex with MUTE to repress SPEECHLESS expression through a local deposition of repressive histone marks. We elucidate the mechanism by which cell-state-specific heterotypic TF complexes facilitate cell-fate commitment by recruiting chromatin modifiers via key co-CREs.
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Affiliation(s)
- Eun-Deok Kim
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Bridget A Fitzgerald
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hyemin Seo
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Krishna Mohan Sepuru
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Soon-Ki Han
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Keiko U Torii
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan.
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24
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Müller-Xing R, Xing Q. The plant stem-cell niche and pluripotency: 15 years of an epigenetic perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:1018559. [PMID: 36388540 PMCID: PMC9659954 DOI: 10.3389/fpls.2022.1018559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Pluripotent stem-cells are slowly dividing cells giving rise to daughter cells that can either differentiate to new tissues and organs, or remain stem-cells. In plants, stem-cells are located in specific niches of the shoot and root apical meristems (SAMs and RAMs). After ablation of stem-cell niches, pluripotent meristematic cells can establish new stem-cells, whereas the removal of the whole meristem destructs the regeneration process. In tissue cultures, after detached plant organs are transferred to rooting or callus induction medium (G5 or CIM), vasculature-associated pluripotent cells (VPCs) immediately start proliferation to form adventitious roots or callus, respectively, while other cell types of the organ explants basically play no part in the process. Hence, in contrast to the widely-held assumption that all plant cells have the ability to reproduce a complete organism, only few cell types are pluripotent in practice, raising the question how pluripotent stem-cells differ from differentiated cells. It is now clear that, in addition to gene regulatory networks of pluripotency factors and phytohormone signaling, epigenetics play a crucial role in initiation, maintenance and determination of plant stem-cells. Although, more and more epigenetic regulators have been shown to control plant stem-cell fate, only a few studies demonstrate how they are recruited and how they change the chromatin structure and transcriptional regulation of pluripotency factors. Here, we highlight recent breakthroughs but also revisited classical studies of epigenetic regulation and chromatin dynamics of plant stem-cells and their pluripotent precursor-cells, and point out open questions and future directions.
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25
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Ye R, Wang M, Du H, Chhajed S, Koh J, Liu KH, Shin J, Wu Y, Shi L, Xu L, Chen S, Zhang Y, Sheen J. Glucose-driven TOR-FIE-PRC2 signalling controls plant development. Nature 2022; 609:986-993. [PMID: 36104568 PMCID: PMC9530021 DOI: 10.1038/s41586-022-05171-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/01/2022] [Indexed: 01/24/2023]
Abstract
Nutrients and energy have emerged as central modulators of developmental programmes in plants and animals1-3. The evolutionarily conserved target of rapamycin (TOR) kinase is a master integrator of nutrient and energy signalling that controls growth. Despite its key regulatory roles in translation, proliferation, metabolism and autophagy2-5, little is known about how TOR shapes developmental transitions and differentiation. Here we show that glucose-activated TOR kinase controls genome-wide histone H3 trimethylation at K27 (H3K27me3) in Arabidopsis thaliana, which regulates cell fate and development6-10. We identify FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), an indispensable component of Polycomb repressive complex 2 (PRC2), which catalyses H3K27me3 (refs. 6-8,10-12), as a TOR target. Direct phosphorylation by TOR promotes the dynamic translocation of FIE from the cytoplasm to the nucleus. Mutation of the phosphorylation site on FIE abrogates the global H3K27me3 landscape, reprogrammes the transcriptome and disrupts organogenesis in plants. Moreover, glucose-TOR-FIE-PRC2 signalling modulates vernalization-induced floral transition. We propose that this signalling axis serves as a nutritional checkpoint leading to epigenetic silencing of key transcription factor genes that specify stem cell destiny in shoot and root meristems and control leaf, flower and silique patterning, branching and vegetative-to-reproduction transition. Our findings reveal a fundamental mechanism of nutrient signalling in direct epigenome reprogramming, with broad relevance for the developmental control of multicellular organisms.
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Affiliation(s)
- Ruiqiang Ye
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Meiyue Wang
- National Key Laboratory of Plant Molecular Genetics, CAS, Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hao Du
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Shweta Chhajed
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Centre for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Kun-Hsiang Liu
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, and Institute of Future Agriculture, Northwest Agriculture and Forestry University, Yangling, China
| | - Jinwoo Shin
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yue Wu
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lin Shi
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS, Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
- Proteomics and Mass Spectrometry, Interdisciplinary Centre for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS, Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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26
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Chen C, Du X. LEAFY COTYLEDONs: Connecting different stages of plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:916831. [PMID: 36119568 PMCID: PMC9470955 DOI: 10.3389/fpls.2022.916831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The life of higher plants progresses successively through embryonic, juvenile, adult, and reproductive stages. LEAFY COTYLEDON (LEC) transcription factors, first discovered in Arabidopsis thaliana several decades ago, play a key role in regulating plant embryonic development, seed maturation, and subsequent growth. Existing studies have demonstrated that LECs together with other transcription factors form a huge and complex regulatory network to regulate many aspects of plant growth and development and respond to environmental stresses. Here, we focus on the role that has received little attention about the LECs linking different developmental stages and generational cycles in plants. We summarize the current fragmented research progress on the LECs role and molecular mechanism in connecting embryonic and vegetative growth periods and the reproductive stage. Furthermore, the possibility of LECs controlling the maintenance and transition of plant growth stages through epigenetic modifications is discussed.
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27
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Zong W, Kim J, Bordiya Y, Qiao H, Sung S. Abscisic acid negatively regulates the Polycomb-mediated H3K27me3 through the PHD-finger protein, VIL1. THE NEW PHYTOLOGIST 2022; 235:1057-1069. [PMID: 35403701 PMCID: PMC9673473 DOI: 10.1111/nph.18156] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/06/2022] [Indexed: 06/12/2023]
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.
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Affiliation(s)
- Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yogendra Bordiya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Hong Qiao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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28
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Liu Y, Bai Y, Li N, Li M, Liu W, Yun DJ, Liu B, Xu ZY. HEXOKINASE1 forms a nuclear complex with the PRC2 subunits CURLY LEAF and SWINGER to regulate glucose signaling. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1168-1180. [PMID: 35394700 DOI: 10.1111/jipb.13261] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
The glucose sensor HEXOKINASE1 (HXK1) integrates myriad external and internal signals to regulate gene expression and development in Arabidopsis thaliana. However, how HXK1 mediates glucose signaling in the nucleus remains unclear. Here, using immunoprecipitation-coupled mass spectrometry, we show that two catalytic subunits of Polycomb Repressive Complex 2, SWINGER (SWN) and CURLY LEAF (CLF), directly interact with catalytically active HXK1 and its inactive forms (HXK1G104D and HXK1S177A ) via their evolutionarily conserved SANT domains. HXK1, CLF, and SWN target common glucose-responsive genes to regulate glucose signaling, as revealed by RNA sequencing. The glucose-insensitive phenotypes of the Arabidopsis swn-1 and clf-50 mutants were similar to that of hxk1, and genetic analysis revealed that CLF, SWN, and HXK1 function in the same genetic pathway. Intriguingly, HXK1 is required for CLF- and SWN-mediated histone H3 lysine 27 (H3K27me3) deposition and glucose-mediated gene repression. Moreover, CLF and SWN affect the recruitment of HXK1 to its target chromatin. These findings support a model in which HXK1 and epigenetic modifiers form a nuclear complex to cooperatively mediate glucose signaling, thereby affecting the histone modification and expression of glucose-regulated genes in plants.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yunshu Bai
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Mengting Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Wenxin Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 132-798, South Korea
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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29
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Forgione I, Muto A, Woloszynska M, Chiappetta AA, Ferrari M, Van Lijsebettens M, Bitonti MB, Bruno L. Epigenetic mechanisms affect the curled leaf phenotype in the hypomethylated ddc mutant of Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111254. [PMID: 35487663 DOI: 10.1016/j.plantsci.2022.111254] [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: 09/21/2021] [Revised: 02/02/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
The ddc mutant of Arabidopsis thaliana is characterized by pleiotropic phenotypic alterations including a curl-shaped leaf, previously explained by disturbed auxin metabolism and transport. The present study was aimed at further explore the molecular bases underlying the abnormal phenotype of the ddc leaf. We demonstrated that genes specifically related to leaf fate commitment and morphogenesis were misexpressed on developing ddc leaves, such as upregulation of CURLY LEAF (CLF) and downregulation of ASYMMETRIC LEAVES2 (AS2), KNOTTED-like gene from A. thaliana (KNAT6), TEOSINTE-LIKE1 CYCLOIDEA and PROLIFERATING CELL FACTOR 2 (TCP2) and others. The CLF gene, encoding a component of Polycomb repressive complex 2 (PRC2) which adds trimethylation marks at Lys27 of histone H3, was overexpressed in the ddc mutant and concomitantly was correlated with DNA methylation-dependent repression of its negative regulator UCL1. KNAT6, encoding a class 1 KNOX homeotic gene, had increased H3K27me3 trimethylation levels, suggesting it is a target gene of the CLF containing PRC2 complex in the ddc mutant. We postulate that different epigenetic mechanisms modulate expression of genes related to auxin pathways as well as gene targets of Polycomb repressive action, during leaf morphogenesis.
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Affiliation(s)
- Ivano Forgione
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium.
| | - Antonella Muto
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
| | - Magdalena Woloszynska
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Genetics, Faculty of Biology and Animal Sciences, Wroclaw University of Environmental and Life Sciences, ul. Kozuchowska 7, 51-631 Wroclaw, Poland.
| | - Adriana Ada Chiappetta
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
| | - Michele Ferrari
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium.
| | - Maria Beatrice Bitonti
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
| | - Leonardo Bruno
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
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30
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Poza-Viejo L, Payá-Milans M, San Martín-Uriz P, Castro-Labrador L, Lara-Astiaso D, Wilkinson MD, Piñeiro M, Jarillo JA, Crevillén P. Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa. PLANT, CELL & ENVIRONMENT 2022; 45:1428-1441. [PMID: 35037269 DOI: 10.1111/pce.14258] [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: 07/05/2021] [Accepted: 12/08/2021] [Indexed: 05/28/2023]
Abstract
Epigenetic regulation is necessary for optimal organism development and preservation of gene expression profiles in the cell. In plants, the trimethylation of histone H3 lysine 27 (H3K27me3) is a silencing epigenetic mark relevant for developmental transitions like flowering. The floral transition is a key agronomic trait; however, the epigenetic mechanisms of flowering time regulation in crops remain poorly understood. Here we study the Jumonji H3K27me3 demethylases BraA.REF6 and BraA.ELF6 in Brassica rapa. Phenotypic characterization of novel mutant lines and genome-wide H3K27me3 chromatin immunoprecipitation and transcriptomic analyses indicated that BraA.REF6 plays a greater role than BraA.ELF6 in fine-tuning H3K27me3 levels. In addition, we found that braA.elf6 mutants were early flowering due to high H3K27me3 levels at B. rapa homologs of the floral repressor FLC. Unlike mutations in Arabidopsis thaliana, braA.ref6 mutants were late flowering without altering the expression of B. rapa FLC genes. Remarkably, we found that BraA.REF6 regulated a number of gibberellic acid (GA) biosynthetic genes, including a homolog of GA1, and that GA-treatment complemented the late flowering mutant phenotype. This study increases our understanding of the epigenetic regulation of flowering time in B. rapa, highlighting conserved and distinct regulatory mechanisms between model and crop species.
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Affiliation(s)
- Laura Poza-Viejo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Miriam Payá-Milans
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Patxi San Martín-Uriz
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Navarra, Spain
| | - Laura Castro-Labrador
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Navarra, Spain
| | - David Lara-Astiaso
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Navarra, Spain
| | - Mark D Wilkinson
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
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Godwin J, Farrona S. The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors. EPIGENOMES 2022; 6:epigenomes6010008. [PMID: 35323212 PMCID: PMC8948837 DOI: 10.3390/epigenomes6010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.
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Nugroho ABD, Lee SW, Pervitasari AN, Moon H, Choi D, Kim J, Kim DH. Transcriptomic and metabolic analyses revealed the modulatory effect of vernalization on glucosinolate metabolism in radish (Raphanus sativus L.). Sci Rep 2021; 11:24023. [PMID: 34912010 PMCID: PMC8674254 DOI: 10.1038/s41598-021-03557-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
Vernalization is the process by which long-term cold like winter triggers transition to flowering in plants. Many biennial and perennial plants including Brassicaceae family plants require vernalization for floral transition. Not only floral transition, but dynamic physiological and metabolic changes might also take place during vernalization. However, vernalization-mediated metabolic change is merely investigated so far. One of secondary metabolites found in Brassiceceae family plants is glucosinolates (GSLs). GSLs provides defense against pathogens and herbivores attack in plants and also exhibits inhibitory activity against human cancer cell. Profiles of GSLs are highly modulated by different environmental stresses in Brassciaceae family plants. To grasp the effect of vernalization on GSLs metabolic dynamics in radish (Raphanus sativus L.), we performed transcriptomic and metabolic analysis during vernalization in radish. Through transcriptome analysis, we found many GSLs metabolic genes were significantly down-regulated by vernalization in radish plants. Ultra-High Performance Liquid Chromatography analysis also revealed that GSLs compounds were substantially reduced in vernalized radish samples compared to non-vernalized radish samples. Furthermore, we found that repressive histone modification (i.e. H3K27me3) is involved in the modulation of GSLs metabolism via epigenetic suppression of Glucoraphasatin Synthase 1 (GRS1) during vernalization in radish. This study revealed that GSLs metabolism is modulated by vernalization, suggestive of a newly identified target of vernalization in radish.
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Affiliation(s)
- Adji Baskoro Dwi Nugroho
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | | | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dasom Choi
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jongkee Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea. .,Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea.
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Xu M, Hu T, Poethig RS. Low light intensity delays vegetative phase change. PLANT PHYSIOLOGY 2021; 187:1177-1188. [PMID: 34618024 PMCID: PMC8566249 DOI: 10.1093/plphys/kiab243] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/07/2021] [Indexed: 05/21/2023]
Abstract
Plants that develop under low light (LL) intensity often display a phenotype known as the "shade tolerance syndrome (STS)". This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development in Arabidopsis (Arabidopsis thaliana). We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase in the expression of the master regulators of vegetative phase change, miR156 and miR157, and a decrease in the expression of their SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) targets. Exogenous sucrose partially corrected the effect of LL on seedling development and miR156 expression. Our results suggest that the response of Arabidopsis to LL is mediated by an increase in miR156/miR157 expression and by factors that repress SPL gene expression independently of miR156/miR157, and is caused in part by a decrease in carbohydrate production. The effect of LL on vegetative phase change does not require the photoreceptors and transcription factors responsible for the shade avoidance syndrome, implying that light intensity and light quality regulate rosette development through different pathways.
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Affiliation(s)
- Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018, USA
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
- Author for communication:
| | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018, USA
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018, USA
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Depuydt T, Vandepoele K. Multi-omics network-based functional annotation of unknown Arabidopsis genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1193-1212. [PMID: 34562334 DOI: 10.1111/tpj.15507] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Unraveling gene function is pivotal to understanding the signaling cascades that control plant development and stress responses. As experimental profiling is costly and labor intensive, there is a clear need for high-confidence computational annotation. In contrast to detailed gene-specific functional information, transcriptomics data are widely available for both model and crop species. Here, we describe a novel automated function prediction method, which leverages complementary information from multiple expression datasets by analyzing study-specific gene co-expression networks. First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n = 15 790) and unknown (n = 11 865) genes in A. thaliana and validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 000 interactions in total), obtaining a set of high-confidence functional annotations. Our method assigned at least one validated annotation to 5054 (42.6%) unknown genes, and at least one novel validated function to 3408 (53.0%) genes with computational annotations only. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help fill the information gap on biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our automated function prediction approach can be applied in future studies to facilitate gene discovery for crop improvement.
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Affiliation(s)
- Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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Bieluszewski T, Xiao J, Yang Y, Wagner D. PRC2 activity, recruitment, and silencing: a comparative perspective. TRENDS IN PLANT SCIENCE 2021; 26:1186-1198. [PMID: 34294542 DOI: 10.1016/j.tplants.2021.06.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/08/2021] [Accepted: 06/16/2021] [Indexed: 05/22/2023]
Abstract
Polycomb repressive complex (PRC)-mediated gene silencing is vital for cell identity and development in both the plant and the animal kingdoms. It also modulates responses to stress. Two major protein complexes, PRC1 and PRC2, execute conserved nuclear functions in metazoans and plants through covalent modification of histones and by compacting chromatin. While a general requirement for Polycomb complexes in mitotically heritable gene repression in the context of chromatin is well established, recent studies have brought new insights into the regulation of Polycomb complex activity and recruitment. Here, we discuss these recent advances with emphasis on PRC2.
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Affiliation(s)
- Tomasz Bieluszewski
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Centre of Excellence for Plant and Microbial Science (CEPAMS), the John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yiman Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19103, USA.
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Kim J, Bordiya Y, Kathare PK, Zhao B, Zong W, Huq E, Sung S. Phytochrome B triggers light-dependent chromatin remodelling through the PRC2-associated PHD finger protein VIL1. NATURE PLANTS 2021; 7:1213-1219. [PMID: 34354260 PMCID: PMC8448934 DOI: 10.1038/s41477-021-00986-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/12/2021] [Indexed: 05/16/2023]
Abstract
To compensate for a sessile nature, plants have developed sophisticated mechanisms to sense varying environmental conditions. Phytochromes (phys) are light and temperature sensors that regulate downstream genes to render plants responsive to environmental stimuli1-4. Here, we show that phyB directly triggers the formation of a repressive chromatin loop by physically interacting with VERNALIZATION INSENSITIVE 3-LIKE1/VERNALIZATION 5 (VIL1/VRN5), a component of Polycomb Repressive Complex 2 (PRC2)5,6, in a light-dependent manner. VIL1 and phyB cooperatively contribute to the repression of growth-promoting genes through the enrichment of Histone H3 Lys27 trimethylation (H3K27me3), a repressive histone modification. In addition, phyB and VIL1 mediate the formation of a chromatin loop to facilitate the repression of ATHB2. Our findings show that phyB directly utilizes chromatin remodelling to regulate the expression of target genes in a light-dependent manner.
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Affiliation(s)
- Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yogendra Bordiya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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Tan C, Ren J, Wang L, Ye X, Fu W, Zhang J, Qi M, Feng H, Liu Z. A single amino acid residue substitution in BraA04g017190.3C, a histone methyltransferase, results in premature bolting in Chinese cabbage (Brassica rapa L. ssp. Pekinensis). BMC PLANT BIOLOGY 2021; 21:373. [PMID: 34388969 PMCID: PMC8361648 DOI: 10.1186/s12870-021-03153-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Flowering is an important inflection point in the transformation from vegetative to reproductive growth, and premature bolting severely decreases crop yield and quality. RESULTS In this study, a stable early-bolting mutant, ebm3, was identified in an ethyl methanesulfonate (EMS)-mutagenized population of a Chinese cabbage doubled haploid (DH) line 'FT'. Compared with 'FT', ebm3 showed early bolting under natural cultivation in autumn, and curled leaves. Genetic analysis showed that the early-bolting phenotype was controlled by a single recessive nuclear gene. Modified MutMap sequencing, genotyping analyses and allelism test provide strong evidence that BrEBM3 (BraA04g017190.3 C), encoding the histone methyltransferase CURLY LEAF (CLF), was the strongly candidate gene of the emb3. A C to T base substitution in the 14th exon of BrEBM3 resulted in an amino acid change (S to F) and the early-bolting phenotype of emb3. The mutation occurred in the SET domain (Suppressor of protein-effect variegation 3-9, Enhancer-of-zeste, Trithorax), which catalyzes site- and state-specific lysine methylation in histones. Tissue-specific expression analysis showed that BrEBM3 was highly expressed in the flower and bud. Promoter activity assay confirmed that BrEBM3 promoter was active in inflorescences. Subcellular localization analysis revealed that BrEBM3 localized in the nucleus. Transcriptomic studies supported that BrEBM3 mutation might repress H3K27me3 deposition and activate expression of the AGAMOUS (AG) and AGAMOUS-like (AGL) loci, resulting in early flowering. CONCLUSIONS Our study revealed that an EMS-induced early-bolting mutant ebm3 in Chinese cabbage was caused by a nonsynonymous mutation in BraA04g017190.3 C, encoding the histone methyltransferase CLF. These results improve our knowledge of the genetic and genomic resources of bolting and flowering, and may be beneficial to the genetic improvement of Chinese cabbage.
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Affiliation(s)
- Chong Tan
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China
| | - Jie Ren
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China
| | - Lin Wang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China
| | - Xueling Ye
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China
| | - Wei Fu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China
| | - Jiamei Zhang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China
| | - Meng Qi
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China
| | - Hui Feng
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China
| | - Zhiyong Liu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, Department of Horticulture, Shenyang Agricultural University, 110866, Shenyang, People's Republic of China.
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Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula. Int J Mol Sci 2021; 22:ijms22147537. [PMID: 34299158 PMCID: PMC8303337 DOI: 10.3390/ijms22147537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/12/2021] [Indexed: 12/20/2022] Open
Abstract
Polycomb group (PcG) proteins, which are important epigenetic regulators, play essential roles in the regulatory networks involved in plant growth, development, and environmental stress responses. Currently, as far as we know, no comprehensive and systematic study has been carried out on the PcG family in Medicago truncatula. In the present study, we identified 64 PcG genes with distinct gene structures from the M. truncatula genome. All of the PcG genes were distributed unevenly over eight chromosomes, of which 26 genes underwent gene duplication. The prediction of protein interaction network indicated that 34 M. truncatula PcG proteins exhibited protein-protein interactions, and MtMSI1;4 and MtVRN2 had the largest number of protein-protein interactions. Based on phylogenetic analysis, we divided 375 PcG proteins from 27 species into three groups and nine subgroups. Group I and Group III were composed of five components from the PRC1 complex, and Group II was composed of four components from the PRC2 complex. Additionally, we found that seven PcG proteins in M. truncatula were closely related to the corresponding proteins of Cicer arietinum. Syntenic analysis revealed that PcG proteins had evolved more conservatively in dicots than in monocots. M. truncatula had the most collinearity relationships with Glycine max (36 genes), while collinearity with three monocots was rare (eight genes). The analysis of various types of expression data suggested that PcG genes were involved in the regulation and response process of M. truncatula in multiple developmental stages, in different tissues, and for various environmental stimuli. Meanwhile, many differentially expressed genes (DEGs) were identified in the RNA-seq data, which had potential research value in further studies on gene function verification. These findings provide novel and detailed information on the M. truncatula PcG family, and in the future it would be helpful to carry out related research on the PcG family in other legumes.
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Post-Embryonic Phase Transitions Mediated by Polycomb Repressive Complexes in Plants. Int J Mol Sci 2021; 22:ijms22147533. [PMID: 34299153 PMCID: PMC8305008 DOI: 10.3390/ijms22147533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Correct timing of developmental phase transitions is critical for the survival and fitness of plants. Developmental phase transitions in plants are partially promoted by controlling relevant genes into active or repressive status. Polycomb Repressive Complex1 (PRC1) and PRC2, originally identified in Drosophila, are essential in initiating and/or maintaining genes in repressive status to mediate developmental phase transitions. Our review summarizes mechanisms in which the embryo-to-seedling transition, the juvenile-to-adult transition, and vegetative-to-reproductive transition in plants are mediated by PRC1 and PRC2, and suggests that PRC1 could act either before or after PRC2, or that they could function independently of each other. Details of the exact components of PRC1 and PRC2 in each developmental phase transitions and how they are recruited or removed will need to be addressed in the future.
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Simonini S, Bemer M, Bencivenga S, Gagliardini V, Pires ND, Desvoyes B, van der Graaff E, Gutierrez C, Grossniklaus U. The Polycomb group protein MEDEA controls cell proliferation and embryonic patterning in Arabidopsis. Dev Cell 2021; 56:1945-1960.e7. [PMID: 34192526 PMCID: PMC8279741 DOI: 10.1016/j.devcel.2021.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/22/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022]
Abstract
Establishing the embryonic body plan of multicellular organisms relies on precisely orchestrated cell divisions coupled with pattern formation, which, in animals, are regulated by Polycomb group (PcG) proteins. The conserved Polycomb Repressive Complex 2 (PRC2) mediates H3K27 trimethylation and comes in different flavors in Arabidopsis. The PRC2 catalytic subunit MEDEA is required for seed development; however, a role for PRC2 in embryonic patterning has been dismissed. Here, we demonstrate that embryos derived from medea eggs abort because MEDEA is required for patterning and cell lineage determination in the early embryo. Similar to PcG proteins in mammals, MEDEA regulates embryonic patterning and growth by controlling cell-cycle progression through repression of CYCD1;1, which encodes a core cell-cycle component. Thus, Arabidopsis embryogenesis is epigenetically regulated by PcG proteins, revealing that the PRC2-dependent modulation of cell-cycle progression was independently recruited to control embryonic cell proliferation and patterning in animals and plants.
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Affiliation(s)
- Sara Simonini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Marian Bemer
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Stefano Bencivenga
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Nuno D Pires
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Bénédicte Desvoyes
- Centro de Biología Molecular Severo Ochoa CSIC-UAM, Nicolás Cabrera 1, Cantoblanco 28049, Madrid, Spain
| | - Eric van der Graaff
- BIOSS Centre for Biological Signaling Studies, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa CSIC-UAM, Nicolás Cabrera 1, Cantoblanco 28049, Madrid, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
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Song J, Xie X, Chen C, Shu J, Thapa RK, Nguyen V, Bian S, Kohalmi SE, Marsolais F, Zou J, Cui Y. LEAFY COTYLEDON1 expression in the endosperm enables embryo maturation in Arabidopsis. Nat Commun 2021; 12:3963. [PMID: 34172749 PMCID: PMC8233312 DOI: 10.1038/s41467-021-24234-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/03/2021] [Indexed: 11/09/2022] Open
Abstract
The endosperm provides nutrients and growth regulators to the embryo during seed development. LEAFY COTYLEDON1 (LEC1) has long been known to be essential for embryo maturation. LEC1 is expressed in both the embryo and the endosperm; however, the functional relevance of the endosperm-expressed LEC1 for seed development is unclear. Here, we provide genetic and transgenic evidence demonstrating that endosperm-expressed LEC1 is necessary and sufficient for embryo maturation. We show that endosperm-synthesized LEC1 is capable of orchestrating full seed maturation in the absence of embryo-expressed LEC1. Inversely, without LEC1 expression in the endosperm, embryo development arrests even in the presence of functional LEC1 alleles in the embryo. We further reveal that LEC1 expression in the endosperm begins at the zygote stage and the LEC1 protein is then trafficked to the embryo to activate processes of seed maturation. Our findings thus establish a key role for endosperm in regulating embryo development.
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Affiliation(s)
- Jingpu Song
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada. .,Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada. .,Department of Biology, Western University, London, ON, Canada.
| | - Xin Xie
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Chen Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada.,Molecular Analysis and Genetic Improvement Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jie Shu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada.,Molecular Analysis and Genetic Improvement Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Raj K Thapa
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Vi Nguyen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Shaomin Bian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,College of Plant Science, Jilin University, Changchun, China
| | | | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada.
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada. .,Department of Biology, Western University, London, ON, Canada.
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42
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Shen Q, Lin Y, Li Y, Wang G. Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues. PLANTS 2021; 10:plants10061165. [PMID: 34201297 PMCID: PMC8228231 DOI: 10.3390/plants10061165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses.
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43
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Current understanding of plant Polycomb group proteins and the repressive histone H3 Lysine 27 trimethylation. Biochem Soc Trans 2021; 48:1697-1706. [PMID: 32725200 DOI: 10.1042/bst20200192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022]
Abstract
Polycomb group (PcG) proteins are highly conserved chromatin-modifying complexes that implement gene silencing in higher eukaryotes. Thousands of genes and multiple developmental processes are regulated by PcG proteins. As the first chromatin modifier been identified in model plant Arabidopsis thaliana, the methyltransferase CURLY LEAF (CLF) and its catalyzed histone H3 Lysine 27 trimethylation (H3K27me3) have already become well-established paradigm in plant epigenetic study. Like in animals, PcG proteins mediate plant development and repress homeotic gene expression by antagonizing with trithorax group proteins. Recent researches have advanced our understanding on plant PcG proteins, including the plant-specific components of these well-conserved protein complexes, the close association with transcription factors and noncoding RNA for the spatial and temporal specificity, the dynamic regulation of the repressive mark H3K27me3 and the PcG-mediated chromatin conformation alterations in gene expression. In this review, we will summarize the molecular mechanisms of PcG-implemented gene repression and the relationship between H3K27me3 and another repressive mark histone H2A Lysine 121 mono-ubiquitination (H2A121ub) will also be discussed.
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44
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Li Z, Luo X, Ou Y, Jiao H, Peng L, Fu X, Macho AP, Liu R, He Y. JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis. MOLECULAR PLANT 2021; 14:732-747. [PMID: 33676023 DOI: 10.1016/j.molp.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/30/2020] [Accepted: 02/27/2021] [Indexed: 05/24/2023]
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 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 during anther and pollen development requires Polycomb proteins at four key regulatory loci. Analysis of genome-wide occupancy of a Polycomb factor and transcriptome reprogramming in response to JA revealed 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.
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Affiliation(s)
- Zicong Li
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China; Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Xiao Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Yang Ou
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China
| | - Huijun Jiao
- Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China; Center for Agroforestry Mega Data Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuehui He
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.
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45
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Dvořák Tomaštíková E, Hafrén A, Trejo-Arellano MS, Rasmussen SR, Sato H, Santos-González J, Köhler C, Hennig L, Hofius D. Polycomb Repressive Complex 2 and KRYPTONITE regulate pathogen-induced programmed cell death in Arabidopsis. PLANT PHYSIOLOGY 2021; 185:2003-2021. [PMID: 33566101 PMCID: PMC8133635 DOI: 10.1093/plphys/kiab035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/08/2021] [Indexed: 05/10/2023]
Abstract
The Polycomb Repressive Complex 2 (PRC2) is well-known for its role in controlling developmental transitions by suppressing the premature expression of key developmental regulators. Previous work revealed that PRC2 also controls the onset of senescence, a form of developmental programmed cell death (PCD) in plants. Whether the induction of PCD in response to stress is similarly suppressed by the PRC2 remained largely unknown. In this study, we explored whether PCD triggered in response to immunity- and disease-promoting pathogen effectors is associated with changes in the distribution of the PRC2-mediated histone H3 lysine 27 trimethylation (H3K27me3) modification in Arabidopsis thaliana. We furthermore tested the distribution of the heterochromatic histone mark H3K9me2, which is established, to a large extent, by the H3K9 methyltransferase KRYPTONITE, and occupies chromatin regions generally not targeted by PRC2. We report that effector-induced PCD caused major changes in the distribution of both repressive epigenetic modifications and that both modifications have a regulatory role and impact on the onset of PCD during pathogen infection. Our work highlights that the transition to pathogen-induced PCD is epigenetically controlled, revealing striking similarities to developmental PCD.
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Affiliation(s)
- Eva Dvořák Tomaštíková
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
- Present address: Institute of Experimental Botany, Czech Academy of Sciences; Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Anders Hafrén
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Minerva S Trejo-Arellano
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
- Present address: Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Sheena Ricafranca Rasmussen
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Hikaru Sato
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Daniel Hofius
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
- Author for communication:
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46
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Shu J, Chen C, Li C, Thapa RK, Song J, Xie X, Nguyen V, Bian S, Liu J, Kohalmi SE, Cui Y. Genome-wide occupancy of Arabidopsis SWI/SNF chromatin remodeler SPLAYED provides insights into its interplay with its close homolog BRAHMA and Polycomb proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:200-213. [PMID: 33432631 DOI: 10.1111/tpj.15159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/26/2020] [Accepted: 01/05/2021] [Indexed: 05/26/2023]
Abstract
SPLAYED (SYD) is a SWItch/Sucrose Non-Fermentable (SWI/SNF)-type chromatin remodeler identified in Arabidopsis thaliana (Arabidopsis). It is believed to play both redundant and differential roles with its closest homolog BRAHMA (BRM) in diverse plant growth and development processes. To better understand how SYD functions, we profiled the genome-wide occupancy of SYD and its impact on the global transcriptome and trimethylation of histone H3 on lysine 27 (H3K27me3). To map the global occupancy of SYD, we generated a GFP-tagged transgenic line and used it for chromatin immunoprecipitation experiments followed by next-generation sequencing, by which more than 6000 SYD target genes were identified. Through integrating SYD occupancy and transcriptome profiles, we found that SYD preferentially targets to nucleosome-free regions of expressed genes. Further analysis revealed that SYD occupancy peaks exhibit five distinct patterns, which were also shared by BRM and BAF60, a conserved SWI/SNF complex component, indicating the common target sites of these SWI/SNF chromatin remodelers and the functional relevance of such distinct patterns. To investigate the interplay between SYD and Polycomb-group (PcG) proteins, we performed a genome-wide analysis of H3K27me3 in syd-5. We observed both increases and decreases in H3K27me3 levels at a few hundred genes in syd-5 compared to wild type. Our results imply that SYD can act antagonistically or synergistically with PcG at specific genes. Together, our SYD genome-wide occupancy data and the transcriptome and H3K27me3 profiles provide a much-needed resource for dissecting SYD's crucial roles in the regulation of plant growth and development.
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Affiliation(s)
- Jie Shu
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Raj K Thapa
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
| | - Jingpu Song
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
| | - Xin Xie
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Jun Liu
- Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | | | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
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47
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Ornelas-Ayala D, Garay-Arroyo A, García-Ponce B, R. Álvarez-Buylla E, Sanchez MDLP. The Epigenetic Faces of ULTRAPETALA1. FRONTIERS IN PLANT SCIENCE 2021; 12:637244. [PMID: 33719312 PMCID: PMC7947857 DOI: 10.3389/fpls.2021.637244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/21/2021] [Indexed: 05/27/2023]
Abstract
ULTRAPETALA1 (ULT1) is a versatile plant-exclusive protein, initially described as a trithorax group (TrxG) factor that regulates transcriptional activation and counteracts polycomb group (PcG) repressor function. As part of TrxG, ULT1 interacts with ARABIDOPSIS TRITHORAX1 (ATX1) to regulate H3K4me3 activation mark deposition. However, our recent studies indicate that ULT1 can also act independently of ATX1. Moreover, the ULT1 ability to interact with transcription factors (TFs) and PcG proteins indicates that it is a versatile protein with other roles. Therefore, in this work we revised recent information about the function of Arabidopsis ULT1 to understand the roles of ULT1 in plant development. Furthermore, we discuss the molecular mechanisms of ULT1, highlighting its epigenetic role, in which ULT1 seems to have characteristics of an epigenetic molecular switch that regulates repression and activation processes via TrxG and PcG complexes.
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Affiliation(s)
- Diego Ornelas-Ayala
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
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48
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Yuan L, Song X, Zhang L, Yu Y, Liang Z, Lei Y, Ruan J, Tan B, Liu J, Li C. The transcriptional repressors VAL1 and VAL2 recruit PRC2 for genome-wide Polycomb silencing in Arabidopsis. Nucleic Acids Res 2021; 49:98-113. [PMID: 33270882 PMCID: PMC7797069 DOI: 10.1093/nar/gkaa1129] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/19/2020] [Accepted: 11/07/2020] [Indexed: 12/11/2022] Open
Abstract
The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. We show that the val1 val2 double mutant possesses somatic embryonic phenotypes and a transcriptome strikingly similar to those of the swn clf double mutant, which lacks the PRC2 catalytic subunits SWINGER (SWN) and CURLY LEAF (CLF). We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. Genome-wide binding profiling demonstrated that they colocalize with SWN and CLF at PRC2 target loci. Loss of VAL1/2 significantly reduces SWN and CLF enrichment at PRC2 target loci and leads to a genome-wide redistribution of H3K27me3 that strongly affects transcription. Finally, we provide evidence that the VAL1/VAL2-RY regulatory system is largely independent of previously identified modules for Polycomb silencing in plants. Together, our work demonstrates an extensive genome-wide interaction between VAL1/2 and PRC2 and provides mechanistic insights into the establishment of Polycomb silencing in plants.
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Affiliation(s)
- Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Lu Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yawen Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Bin Tan
- Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510624, China
| | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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49
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Yin X, Romero-Campero FJ, de Los Reyes P, Yan P, Yang J, Tian G, Yang X, Mo X, Zhao S, Calonje M, Zhou Y. H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots. Nat Commun 2021; 12:315. [PMID: 33436613 PMCID: PMC7804394 DOI: 10.1038/s41467-020-20614-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/07/2020] [Indexed: 02/02/2023] Open
Abstract
Although it is well established that the Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin accessibility, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that PcG function regulates chromatin accessibility. We find that H2AK121ub is associated with a less accessible but still permissive chromatin at transcriptional regulation hotspots. Accessibility is further reduced by EMF1 acting in collaboration with PRC2 activity. Consequently, H2AK121ub/H3K27me3 marks are linked to inaccessible although responsive chromatin. In contrast, only-H3K27me3-marked chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Nevertheless, despite the loss of PcG activities leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that accessible chromatin is not always predictive of gene expression.
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Affiliation(s)
- Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Francisco J Romero-Campero
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092, Seville, Spain.
- Department of Computer Science and Artificial Intelligence (University of Sevilla), Avenida Reina Mercedes s/n, 41012, Seville, Spain.
| | - Pedro de Los Reyes
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Peng Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, 310058, Hangzhou, China
| | - Jing Yang
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Guangmei Tian
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - XiaoZeng Yang
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, 310058, Hangzhou, China
| | - Shuangshuang Zhao
- Key Laboratory of Plant Stress, Life Science College, Shandong Normal University, 250014, Jinan, China
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092, Seville, Spain.
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
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50
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Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li Z, Zouine M, Bouzayen M. Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato. THE NEW PHYTOLOGIST 2021; 229:902-919. [PMID: 32875585 PMCID: PMC7821339 DOI: 10.1111/nph.16902] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 05/10/2023]
Abstract
Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower-to-fruit transition remains poor. We investigated the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations.
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Affiliation(s)
- Guojian Hu
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Baowen Huang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Keke Wang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Pierre Frasse
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Elie Maza
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Anis Djari
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris‐SaclayCNRSINRAUniversity Paris‐SudUniversity of EvryUniversity Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayBatiment 630Orsay91405France
| | - Philippe Gallusci
- UMR EGFVBordeaux Sciences AgroINRAUniversité de Bordeaux210 Chemin de Leysotte, CS 50008Villenave d’Ornon33882France
| | - Zhengguo Li
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
| | - Mohamed Zouine
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Mondher Bouzayen
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
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