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Xu H, Chen X, Zeng G, Qin X, Deng Z, Cheng W, Shen X, Hu Y. Unveiling common and specific features of the COMPASS-like complex in sorghum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108709. [PMID: 38744082 DOI: 10.1016/j.plaphy.2024.108709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
The COMPASS-like complex, responsible for depositing H3K4 methylation, exhibits a conserved composition across yeast, plants, and animals, with functional analysis highlighting its crucial roles in plant development and stress response. In this study, we identified nine genes encoding four subunits of the COMPASS-like complex through homologous search. Phylogenetic analysis revealed the presence of two additional ASH2 genes in the sorghum genome, specifically expressed in endosperms, suggesting the formation of a unique COMPASS-like complex in sorghum endosperms. Y2H and BiFC protein-protein interaction tests demonstrated the interaction between SbRbBP5 and SbASH2A/B/C, while the association between other subunits appeared weak, possibly due to sequence variations in SbWDR5 or synergistic interactions among COMPASS-like complex subunits. The interaction between ATX1 and the C-Terminal Domain (CTD) of Pol II, reported in Arabidopsis, was not detected in sorghum. However, we made the novel discovery of transcriptional activation activity in RbBP5, which is conserved in sorghum, rice, and Arabidopsis, providing valuable insights into the mechanism by which the COMPASS-like complex regulates gene expression in plants.
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Affiliation(s)
- Huan Xu
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China; Jingchu University of Technology, Jingmen, Hubei, 448000, China
| | - Xiaoliang Chen
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Gongjian Zeng
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Xiner Qin
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Zhuying Deng
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Wenhan Cheng
- Jingchu University of Technology, Jingmen, Hubei, 448000, China
| | - Xiangling Shen
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China.
| | - Yongfeng Hu
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China.
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2
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Lu Q, Shi W, Zhang F, Ding Y. ATX1 and HUB1/2 promote recruitment of the transcription elongation factor VIP2 to modulate the floral transition in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1760-1773. [PMID: 38446797 DOI: 10.1111/tpj.16707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/14/2024] [Accepted: 01/27/2024] [Indexed: 03/08/2024]
Abstract
Histone 2B ubiquitination (H2Bub) and trimethylation of H3 at lysine 4 (H3K4me3) are associated with transcription activation. However, the function of these modifications in transcription in plants remains largely unknown. Here, we report that coordination of H2Bub and H3K4me3 deposition with the binding of the RNA polymerase-associated factor VERNALIZATION INDEPENDENCE2 (VIP2) to FLOWERING LOCUS C (FLC) modulates flowering time in Arabidopsis. We found that RING domain protein HISTONE MONOUBIQUITINATION1 (HUB1) and HUB2 (we refer as HUB1/2), which are responsible for H2Bub, interact with ARABIDOPSIS TRITHORAX1 (ATX1), which is required for H3K4me3 deposition, to promote the transcription of FLC and repress the flowering time. The atx1-2 hub1-10 hub2-2 triple mutant in FRIGIDIA (FRI) background displayed early flowering like FRI hub1-10 hub2-2 and overexpression of ATX1 failed to rescue the early flowering phenotype of hub1-10 hub2-2. Mutations in HUB1 and HUB2 reduced the ATX1 enrichment at FLC, indicating that HUB1 and HUB2 are required for ATX1 recruitment and H3K4me3 deposition at FLC. We also found that the VIP2 directly binds to HUB1, HUB2, and ATX1 and that loss of VIP2 in FRI hub1-10 hub2-2 and FRI atx1-2 plants resulted in early flowering like that observed in FRI vip2-10. Loss of function of HUB2 and ATX1 impaired VIP2 enrichment at FLC, and reduced the transcription initiation and elongation of FLC. In addition, mutations in VIP2 reduced HUB1 and ATX1 enrichment and H2Bub and H3K4me3 levels at FLC. Together, our findings revealed that HUB1/2, ATX1, and VIP2 coordinately modulate H2Bub and H3K4me3 deposition, FLC transcription, and flowering time.
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Affiliation(s)
- Qianqian Lu
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Wenwen Shi
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Fei Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Yong Ding
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
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3
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Zhang B, Wang Z, Dai X, Gao J, Zhao J, Ma R, Chen Y, Sun Y, Ma H, Li S, Zhou C, Wang JP, Li W. A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa. THE NEW PHYTOLOGIST 2024; 241:1950-1972. [PMID: 38095236 DOI: 10.1111/nph.19481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Histone H3 lysine-4 trimethylation (H3K4me3) activating drought-responsive genes in plants for drought adaptation has long been established, but the underlying regulatory mechanisms are unknown. Here, using yeast two-hybrid, bimolecular fluorescence complementation, biochemical analyses, transient and CRISPR-mediated transgenesis in Populus trichocarpa, we unveiled in this adaptation a regulatory interplay between chromatin regulation and gene transactivation mediated by an epigenetic determinant, a PtrSDG2-1-PtrCOMPASS (complex proteins associated with Set1)-like H3K4me3 complex, PtrSDG2-1-PtrWDR5a-1-PtrRbBP5-1-PtrAsh2-2 (PtrSWRA). Under drought conditions, a transcription factor PtrAREB1-2 interacts with PtrSWRA, forming a PtrSWRA-PtrAREB1-2 pentamer, to recruit PtrSWRA to specific promoter elements of drought-tolerant genes, such as PtrHox2, PtrHox46, and PtrHox52, for depositing H3K4me3 to promote and maintain activated state of such genes for tolerance. CRISPR-edited defects in the pentamer impaired drought tolerance and elevated expression of PtrHox2, PtrHox46, or PtrHox52 improved the tolerance as well as growth in P. trichocarpa. Our findings revealed the identity of the underlying H3K4 trimethyltransferase and its interactive arrangement with the COMPASS for catalysis specificity and efficiency. Furthermore, our study uncovered how the H3K4 trimethyltransferase-COMPASS complex is recruited to the effector genes for elevating H3K4me3 marks for improved drought tolerance and growth/biomass production in plants.
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Affiliation(s)
- Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfeng Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Rong Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yanjie Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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Ost C, Cao HX, Nguyen TL, Himmelbach A, Mascher M, Stein N, Humbeck K. Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes. Int J Mol Sci 2023; 24:12065. [PMID: 37569441 PMCID: PMC10418636 DOI: 10.3390/ijms241512065] [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: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach.
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Affiliation(s)
- Charlotte Ost
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Thuy Linh Nguyen
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Göttingen, Germany
| | - Klaus Humbeck
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
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5
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Ji X, Liu W, Zhang F, Su Y, Ding Y, Li H. H3K36me3 and H2A.Z coordinately modulate flowering time in Arabidopsis. J Genet Genomics 2023:S1673-8527(23)00122-4. [PMID: 37302474 DOI: 10.1016/j.jgg.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Affiliation(s)
- Xiaoru Ji
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei, Anhui 230027, China; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Hefei, Anhui 230027, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wenqian Liu
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fei Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei, Anhui 230027, China; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Hefei, Anhui 230027, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yanhua Su
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei, Anhui 230027, China; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Hefei, Anhui 230027, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yong Ding
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei, Anhui 230027, China; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Hefei, Anhui 230027, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
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García-Murillo L, Valencia-Lozano E, Priego-Ranero NA, Cabrera-Ponce JL, Duarte-Aké FP, Vizuet-de-Rueda JC, Rivera-Toro DM, Herrera-Ubaldo H, de Folter S, Alvarez-Venegas R. CRISPRa-mediated transcriptional activation of the SlPR-1 gene in edited tomato plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111617. [PMID: 36731748 DOI: 10.1016/j.plantsci.2023.111617] [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: 08/29/2022] [Revised: 01/11/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
With the continuous deterioration of arable land due to an ever-growing population, improvement of crops and crop protection have a fundamental role in maintaining and increasing crop productivity. Alternatives to the use of pesticides encompass the use of biological control agents, generation of new resistant crop cultivars, the application of plant activator agrochemicals to enhance plant defenses, and the use of gene editing techniques, like the CRISPR-Cas system. Here, we test the hypothesis that epigenome editing, via CRISPR activation (CRISPRa), activate tomato plant defense genes to confer resistance against pathogen attack. We provide evidence that edited tomato plants for the PATHOGENESIS-RELATED GENE 1 gene (SlPR-1) show enhanced disease resistance to Clavibacter michiganensis subsp. michiganensis infection. Resistance was assessed by evaluating disease progression and symptom appearance, pathogen accumulation, and changes in SlPR-1 gene expression at different time points. We determined that CRISPRa-edited plants develop enhanced disease-resistant to the pathogen without altering their agronomic characteristics and, above all, preventing the advancement of disease symptoms, stem canker, and plant death.
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Affiliation(s)
- Leonardo García-Murillo
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Eliana Valencia-Lozano
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Nicolás Alberto Priego-Ranero
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - José Luis Cabrera-Ponce
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Fátima Patricia Duarte-Aké
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Juan Carlos Vizuet-de-Rueda
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Diana Marcela Rivera-Toro
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Humberto Herrera-Ubaldo
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Raúl Alvarez-Venegas
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico.
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Ma YS, Jie HD, Zhao L, Lv XY, Liu XC, Tang YY, Zhang Y, He PL, Xing HC, Jie YC. Identification of the Xyloglucan Endotransglycosylase/Hydrolase ( XTH) Gene Family Members Expressed in Boehmeria nivea in Response to Cadmium Stress. Int J Mol Sci 2022; 23:ijms232416104. [PMID: 36555743 PMCID: PMC9785722 DOI: 10.3390/ijms232416104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Xyloglucan endotransglycosylase/hydrolase (XTH) genes play an important role in plant resistance to abiotic stress. However, systematic studies of the response of Boehmeria nivea (ramie) XTH genes (BnXTHs) to cadmium (Cd) stress are lacking. We sought to identify the BnXTH-family genes in ramie through bioinformatics analyses and to investigate their responses to Cd stress. We identified 19 members of the BnXTH gene family from the ramie genome, referred to as BnXTH1-19, among which BnXTH18 and BnXTH19 were located on no chromosomes and the remaining genes were unevenly distributed across 11 chromosomes. The 19 members were divided into four groups, Groups I/II/IIIA/IIIB, according to their phylogenetic relationships, and these groups were supported by analyses of intron-exon structure and conserved motif composition. A highly conserved catalytic site (HDEIDFEFLG) was observed in all BnXTH proteins. Additionally, three gene pairs (BnXTH6-BnXTH16, BnXTH8-BnXTH9, and BnXTH17-BnXTH18) were obtained with a fragment and tandem-repeat event analysis of the ramie genome. An analysis of cisregulatory elements revealed that BnXTH expression might be regulated by multiple hormones and abiotic and biotic stress responses. In particular, 17 cisregulatory elements related to abiotic and biotic stress responses and 11 cisregulatory elements related to hormone responses were identified. We also found that most BnXTH genes responded to Cd stress, and BnXTH1, BnXTH3, BnXTH6, and BnXTH15 were most likely to contribute to the Cd tolerance of ramie, as evidenced by the substantial increases in expression under Cd treatment. Heterologous expression of BnXTH1, BnXTH6, and BnXTH15 significantly enhanced the Cd tolerance of transgenic yeast cells. These results suggest that the BnXTH gene family is involved in Cd stress responses, laying a theoretical foundation for functional studies of BnXTH genes and the innovative breeding of Cd-tolerant ramie.
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Affiliation(s)
- Yu-Shen Ma
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hong-Dong Jie
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Long Zhao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xue-Ying Lv
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xiao-Chun Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yan-Yi Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Ying Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Peng-Liang He
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hu-Cheng Xing
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Engineering Research Center for Grass Crop Germplasm Innovation and Utilization, Changsha 410128, China
| | - Yu-Cheng Jie
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Engineering Research Center for Grass Crop Germplasm Innovation and Utilization, Changsha 410128, China
- Correspondence:
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Zhang D, Guo W, Wang T, Wang Y, Le L, Xu F, Wu Y, Wuriyanghan H, Sung ZR, Pu L. RNA 5-Methylcytosine Modification Regulates Vegetative Development Associated with H3K27 Trimethylation in Arabidopsis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2204885. [PMID: 36382558 PMCID: PMC9811455 DOI: 10.1002/advs.202204885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Methylating RNA post-transcriptionally is emerging as a significant mechanism of gene regulation in eukaryotes. The crosstalk between RNA methylation and histone modification is critical for chromatin state and gene expression in mammals. However, it is not well understood mechanistically in plants. Here, the authors report a genome-wide correlation between RNA 5-cytosine methylation (m5 C) and histone 3 lysine27 trimethylation (H3K27me3) in Arabidopsis. The plant-specific Polycomb group (PcG) protein EMBRYONIC FLOWER1 (EMF1) plays dual roles as activators or repressors. Transcriptome-wide RNA m5 C profiling revealed that m5 C peaks are mostly enriched in chromatin regions that lacked H3K27me3 in both wild type and emf1 mutants. EMF1 repressed the expression of m5 C methyltransferase tRNA specific methyltransferase 4B (TRM4B) through H3K4me3, independent of PcG-mediated H3K27me3 mechanism. The 5-Cytosine methylation on targets is increased in emf1 mutants, thereby decreased the mRNA transcripts of photosynthesis and chloroplast genes. In addition, impairing EMF1 activity reduced H3K27me3 levels of PcG targets, such as starch genes, which are de-repressed in emf1 mutants. Both EMF1-mediated promotion and repression of gene activities via m5 C and H3K27me3 are required for normal vegetative growth. Collectively, t study reveals a previously undescribed epigenetic mechanism of RNA m5 C modifications and histone modifications to regulate gene expression in eukaryotes.
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Affiliation(s)
- Daolei Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
- School of Life ScienceInner Mongolia UniversityHohhot010021P. R. China
| | - Weijun Guo
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Ting Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
- Shangrao Normal UniversityShangrao334001P. R. China
| | - Yifan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Liang Le
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Fan Xu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Yue Wu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Hada Wuriyanghan
- School of Life ScienceInner Mongolia UniversityHohhot010021P. R. China
| | - Zinmay Renee Sung
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCA94720USA
| | - Li Pu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
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9
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Oya S, Takahashi M, Takashima K, Kakutani T, Inagaki S. Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation. Nat Commun 2022; 13:4521. [PMID: 35953471 PMCID: PMC9372134 DOI: 10.1038/s41467-022-32165-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.
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Affiliation(s)
- Satoyo Oya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | | | | | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- National Institute of Genetics, Mishima, Japan.
| | - Soichi Inagaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
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10
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Wang S, Zhang F, Jiang P, Zhang H, Zheng H, Chen R, Xu Z, Ikram AU, Li E, Xu Z, Fan J, Su Y, Ding Y. SDG128 is involved in maize leaf inclination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1597-1608. [PMID: 34612535 DOI: 10.1111/tpj.15527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/04/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Maize leaf angle (LA) is a complex quantitative trait that is controlled by developmental signals, hormones, and environmental factors. However, the connection between histone methylation and LAs in maize remains unclear. Here, we reported that SET domain protein 128 (SDG128) is involved in leaf inclination in maize. Knockdown of SDG128 using an RNA interference approach resulted in an expanded architecture, less large vascular bundles, more small vascular bundles, and larger spacing of large vascular bundles in the auricles. SDG128 interacts with ZmGID2 both in vitro and in vivo. Knockdown of ZmGID2 also showed a larger LA with less large vascular bundles and larger spacing of vascular bundles. In addition, the transcription level of cell wall expansion family genes ZmEXPA1, ZmEXPB2, and GRMZM2G005887; transcriptional factor genes Lg1, ZmTAC1, and ZmCLA4; and auxin pathway genes ZmYUCCA7, ZmYUCCA8, and ZmARF22 was reduced in SDG128 and ZmGID2 knockdown plants. SDG128 directly targets ZmEXPA1, ZmEXPB2, LG1, and ZmTAC1 and is required for H3K4me3 deposition at these genes. Together, the results of the present study suggest that SDG128 and ZmGID2 are involved in the maize leaf inclination.
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Affiliation(s)
- Shiliang Wang
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Fei Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Pengfei Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Heng Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Han Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Rihong Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Zuntao Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Aziz Ul Ikram
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Enze Li
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Zaoshi Xu
- Anhui Forestry High-Tech Development Center, Hefei, Anhui, 230041, China
| | - Jun Fan
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yanhua Su
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Yong Ding
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
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11
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Fang H, Shao Y, Wu G. Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction. FRONTIERS IN PLANT SCIENCE 2021; 12:782450. [PMID: 34917115 PMCID: PMC8669150 DOI: 10.3389/fpls.2021.782450] [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: 09/24/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Plants undergo extensive reprogramming of chromatin status during sexual reproduction, a process vital to cell specification and pluri- or totipotency establishment. As a crucial way to regulate chromatin organization and transcriptional activity, histone modification can be reprogrammed during sporogenesis, gametogenesis, and embryogenesis in flowering plants. In this review, we first introduce enzymes required for writing, recognizing, and removing methylation marks on lysine residues in histone H3 tails, and describe their differential expression patterns in reproductive tissues, then we summarize their functions in the reprogramming of H3 lysine methylation and the corresponding chromatin re-organization during sexual reproduction in Arabidopsis, and finally we discuss the molecular significance of histone reprogramming in maintaining the pluri- or totipotency of gametes and the zygote, and in establishing novel cell fates throughout the plant life cycle. Despite rapid achievements in understanding the molecular mechanism and function of the reprogramming of chromatin status in plant development, the research in this area still remains a challenge. Technological breakthroughs in cell-specific epigenomic profiling in the future will ultimately provide a solution for this challenge.
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12
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Shang FHZ, Liu HN, Wan YT, Yu YH, Guo DL. Identification of grape H3K4 genes and their expression profiles during grape fruit ripening and postharvest ROS treatment. Genomics 2021; 113:3793-3803. [PMID: 34534647 DOI: 10.1016/j.ygeno.2021.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Fruit development is modified by different types of epigenetics. Histone methylation is an important way of epigenetic modification. Eight genes related to H3K4 methyltransferase, named VvH3K4s, were identified and isolated from the grape genome based on conserved domain analysis, which could be divided into 3 categories by the phylogenetic relationship. Transcriptome data showed that VvH3K4-5 was obviously up-regulated during fruit ripe, and its expression level was significantly different between 'Kyoho' and 'Fengzao'. The VvH3K4s promoters contains cis-acting elements of in response to stress, indicating that they may be involved in the metabolic pathways regulated by ROS signaling. The subcellular localization experiment and promoter activity analysis experiment on VvH3K4-5 showed that VvH3K4s may be regulated by H2O2. With H2O2 and Hypotaurine treatment, it was found that the expression pattern of most genes was opposite, and the expression level showed different expression trend with the extension of treatment time.
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Affiliation(s)
- Fang-Hui-Zi Shang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, PR China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, PR China
| | - Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, PR China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, PR China
| | - Yu-Tong Wan
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, PR China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, PR China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, PR China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, PR China
| | - Da-Long Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, PR China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, PR China.
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13
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Song ZT, Zhang LL, Han JJ, Zhou M, Liu JX. Histone H3K4 methyltransferases SDG25 and ATX1 maintain heat-stress gene expression during recovery in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1326-1338. [PMID: 33278042 DOI: 10.1111/tpj.15114] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Plants have short-term stress memory that enables them to maintain the expression state of a substantial subset of heat-inducible genes during stress recovery after heat stress. Little is known about the molecular mechanisms controlling stress-responsive gene expression at the recovery stage in plants, however. In this article, we demonstrate that histone H3K4 methyltransferases SDG25 and ATX1 are required for heat-stress tolerance in Arabidopsis. SDG25 and ATX1 are not only important for stress-responsive gene expression during heat stress, but also for maintaining stress-responsive gene expression during stress recovery. A combination of whole-genome bisulfite sequencing, RNA-sequencing and ChIP-qPCR demonstrated that mutations of SDG25 and ATX1 decrease histone H3K4me3 levels, increase DNA cytosine methylation and inhibit the expression of a subset of heat stress-responsive genes during stress recovery in Arabidopsis. ChIP-qPCR results confirm that ATX1 binds to chromatins associated with these target genes. Our results reveal that histone H3K4me3 affects DNA methylation at regions in the loci associated with heat stress-responsive gene expression during stress recovery, providing insights into heat-stress transcriptional memory in plants.
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Affiliation(s)
- Ze-Ting Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Lin-Lin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jia-Jia Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
| | - Ming Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
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14
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Foroozani M, Vandal MP, Smith AP. H3K4 trimethylation dynamics impact diverse developmental and environmental responses in plants. PLANTA 2021; 253:4. [PMID: 33387051 DOI: 10.1007/s00425-020-03520-0] [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: 07/19/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The H3K4me3 histone mark in plants functions in the regulation of gene expression and transcriptional memory, and influences numerous developmental processes and stress responses. Plants execute developmental programs and respond to changing environmental conditions via adjustments in gene expression, which are modulated in part by chromatin structure dynamics. Histone modifications alter chromatin in precise ways on a global scale, having the potential to influence the expression of numerous genes. Trimethylation of lysine 4 on histone H3 (H3K4me3) is a prominent histone modification that is dogmatically associated with gene activity, but more recently has also been linked to gene repression. As in other eukaryotes, the distribution of H3K4me3 in plant genomes suggests it plays a central role in gene expression regulation, however the underlying mechanisms are not fully understood. Transcript levels of many genes related to flowering, root, and shoot development are affected by dynamic H3K4me3 levels, as are those for a number of stress-responsive and stress memory-related genes. This review examines the current understanding of how H3K4me3 functions in modulating plant responses to developmental and environmental cues.
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Affiliation(s)
- Maryam Foroozani
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Matthew P Vandal
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
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15
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Zhang YZ, Yuan J, Zhang L, Chen C, Wang Y, Zhang G, Peng L, Xie SS, Jiang J, Zhu JK, Du J, Duan CG. Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis. Nat Commun 2020; 11:6212. [PMID: 33277495 PMCID: PMC7718874 DOI: 10.1038/s41467-020-20089-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023] Open
Abstract
Histone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, in Arabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector gene ARGONAUTE 5 (AGO5). We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing.
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Affiliation(s)
- Yi-Zhe Zhang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jianlong Yuan
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Lingrui Zhang
- grid.169077.e0000 0004 1937 2197Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Chunxiang Chen
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Yuhua Wang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Guiping Zhang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Li Peng
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Si-Si Xie
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jing Jiang
- grid.256922.80000 0000 9139 560XState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Jian-Kang Zhu
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.169077.e0000 0004 1937 2197Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Jiamu Du
- grid.263817.9Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Cheng-Guo Duan
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.256922.80000 0000 9139 560XState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
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16
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Rehman M, Tanti B. Understanding epigenetic modifications in response to abiotic stresses in plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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17
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Antosz W, Deforges J, Begcy K, Bruckmann A, Poirier Y, Dresselhaus T, Grasser KD. Critical Role of Transcript Cleavage in Arabidopsis RNA Polymerase II Transcriptional Elongation. THE PLANT CELL 2020; 32:1449-1463. [PMID: 32152189 PMCID: PMC7203918 DOI: 10.1105/tpc.19.00891] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/10/2020] [Accepted: 03/05/2020] [Indexed: 05/14/2023]
Abstract
Transcript elongation factors associate with elongating RNA polymerase II (RNAPII) to control the efficiency of mRNA synthesis and consequently modulate plant growth and development. Encountering obstacles during transcription such as nucleosomes or particular DNA sequences may cause backtracking and transcriptional arrest of RNAPII. The elongation factor TFIIS stimulates the intrinsic transcript cleavage activity of the polymerase, which is required for efficient rescue of backtracked/arrested RNAPII. A TFIIS mutant variant (TFIISmut) lacks the stimulatory activity to promote RNA cleavage, but instead efficiently inhibits unstimulated transcript cleavage by RNAPII. We could not recover viable Arabidopsis (Arabidopsis thaliana) tfIIs plants constitutively expressing TFIISmut. Induced, transient expression of TFIISmut in tfIIs plants provoked severe growth defects, transcriptomic changes and massive, transcription-related redistribution of elongating RNAPII within transcribed regions toward the transcriptional start site. The predominant site of RNAPII accumulation overlapped with the +1 nucleosome, suggesting that upon inhibition of RNA cleavage activity, RNAPII arrest prevalently occurs at this position. In the presence of TFIISmut, the amount of RNAPII was reduced, which could be reverted by inhibiting the proteasome, indicating proteasomal degradation of arrested RNAPII. Our findings suggest that polymerase backtracking/arrest frequently occurs in plant cells, and RNAPII-reactivation is essential for correct transcriptional output and proper growth/development.
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Affiliation(s)
- Wojciech Antosz
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, Florida 32611
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Dresselhaus
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
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18
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Zhang X, Ménard R, Li Y, Coruzzi GM, Heitz T, Shen WH, Berr A. Arabidopsis SDG8 Potentiates the Sustainable Transcriptional Induction of the Pathogenesis-Related Genes PR1 and PR2 During Plant Defense Response. FRONTIERS IN PLANT SCIENCE 2020; 11:277. [PMID: 32218796 PMCID: PMC7078350 DOI: 10.3389/fpls.2020.00277] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/21/2020] [Indexed: 05/23/2023]
Abstract
Post-translational covalent modifications of histones play important roles in modulating chromatin structure and are involved in the control of multiple developmental processes in plants. Here we provide insight into the contribution of the histone lysine methyltransferase SET DOMAIN GROUP 8 (SDG8), implicated in histone H3 lysine 36 trimethylation (H3K36me3), in connection with RNA polymerase II (RNAPII) to enhance Arabidopsis immunity. We showed that even if the sdg8-1 loss-of-function mutant, defective in H3K36 methylation, displayed a higher sensitivity to different strains of the bacterial pathogen Pseudomonas syringae, effector-triggered immunity (ETI) still operated, but less efficiently than in the wild-type (WT) plants. In sdg8-1, the level of the plant defense hormone salicylic acid (SA) was abnormally high under resting conditions and was accumulated similarly to WT at the early stage of pathogen infection but quickly dropped down at later stages. Concomitantly, the transcription of several defense-related genes along the SA signaling pathway was inefficiently induced in the mutant. Remarkably, albeit the defense genes PATHOGENESIS-RELATED1 (PR1) and PR2 have retained responsiveness to exogenous SA, their inductions fade more rapidly in sdg8-1 than in WT. At chromatin, while global levels of histone methylations were found to be stable, local increases of H3K4 and H3K36 methylations as well as RNAPII loading were observed at some defense genes following SA-treatments in WT. In sdg8-1, the H3K36me3 increase was largely attenuated and also the increases of H3K4me3 and RNAPII were frequently compromised. Lastly, we demonstrated that SDG8 could physically interact with the RNAPII C-terminal Domain, providing a possible link between RNAPII loading and H3K36me3 deposition. Collectively, our results indicate that SDG8, through its histone methyltransferase activity and its physical coupling with RNAPII, participates in the strong transcriptional induction of some defense-related genes, in particular PR1 and PR2, to potentiate sustainable immunity during plant defense response to bacterial pathogen.
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Affiliation(s)
- Xue Zhang
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Rozenn Ménard
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Gloria M. Coruzzi
- Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY, United States
| | - Thierry Heitz
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
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19
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The Trithorax Group Factor ULTRAPETALA1 Regulates Developmental as Well as Biotic and Abiotic Stress Response Genes in Arabidopsis. G3-GENES GENOMES GENETICS 2019; 9:4029-4043. [PMID: 31604825 PMCID: PMC6893208 DOI: 10.1534/g3.119.400559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In eukaryotes, Polycomb group (PcG) and trithorax group (trxG) factors oppositely regulate gene transcription during development through histone modifications, with PcG factors repressing and trxG factors activating the expression of their target genes. Although plant trxG factors regulate many developmental and physiological processes, their downstream targets are poorly characterized. Here we use transcriptomics to identify genome-wide targets of the Arabidopsis thaliana trxG factor ULTRAPETALA1 (ULT1) during vegetative and reproductive development and compare them with those of the PcG factor CURLY LEAF (CLF). We find that genes involved in development and transcription regulation are over-represented among ULT1 target genes. In addition, stress response genes and defense response genes such as those in glucosinolate metabolic pathways are enriched, revealing a previously unknown role for ULT1 in controlling biotic and abiotic response pathways. Finally, we show that many ULT1 target genes can be oppositely regulated by CLF, suggesting that ULT1 and CLF may have antagonistic effects on plant growth and development in response to various endogenous and environmental cues.
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20
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Jing Y, Guo Q, Lin R. The Chromatin-Remodeling Factor PICKLE Antagonizes Polycomb Repression of FT to Promote Flowering. PLANT PHYSIOLOGY 2019; 181:656-668. [PMID: 31377725 PMCID: PMC6776858 DOI: 10.1104/pp.19.00596] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/16/2019] [Indexed: 05/19/2023]
Abstract
Changing daylength (or photoperiod) is a seasonal cue used by many plants to adjust the timing of their floral transition to ensure reproductive success. An inductive long-day photoperiod triggers the expression of FLOWERING LOCUS T (FT), which promotes flowering. FT, encoding a major component of florigen, is induced in leaf veins specifically at dusk through the photoperiod pathway; however, the modulation of FT expression in response to photoperiod cues remains poorly understood. Here, we report that the balance between Polycomb group (PcG) and Trithorax group (TrxG) proteins sets appropriate FT expression in long days in Arabidopsis (Arabidopsis thaliana). In PcG mutant lines, FT was highly derepressed, but FT expression was decreased to an almost wild-type level and pattern upon the additional disruption of chromatin-remodeling factors PICKLE (PKL) and ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), but not by disruption of photoperiod pathway components. PKL interacts with ATX1 to mediate trimethylation of histone H3 on lysine-4 at the FT locus, leading to antagonistic effects of PKL and ATX1 on PcG proteins in the regulation of FT expression. Therefore, the TrxG-like protein PKL prevents PcG-mediated silencing to ensure specific and appropriate expression of FT, thereby determining the proper flowering response.
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Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qiang Guo
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100093, China
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21
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Song Q, Huang TY, Yu HH, Ando A, Mas P, Ha M, Chen ZJ. Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis. Genome Biol 2019; 20:170. [PMID: 31429787 PMCID: PMC6892391 DOI: 10.1186/s13059-019-1777-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/29/2019] [Indexed: 11/23/2022] Open
Abstract
Background Circadian rhythms modulate growth and development in all organisms through interlocking transcriptional-translational feedback loops. The transcriptional loop involves chromatin modifications of central circadian oscillators in mammals and plants. However, the molecular basis for rhythmic epigenetic modifications and circadian regulation is poorly understood. Results Here we report a feedback relationship between diurnal regulation of circadian clock genes and histone modifications in Arabidopsis. On one hand, the circadian oscillators CCA1 and LHY regulate diurnal expression of genes coding for the eraser (JMJ14) directly and writer (SDG2) indirectly for H3K4me3 modification, leading to rhythmic H3K4me3 changes in target genes. On the other hand, expression of circadian oscillator genes including CCA1 and LHY is associated with H3K4me3 levels and decreased in the sdg2 mutant but increased in the jmj14 mutant. At the genome-wide level, diurnal rhythms of H3K4me3 and another histone mark H3K9ac are associated with diurnal regulation of 20–30% of the expressed genes. While the majority (86%) of H3K4me3 and H3K9ac target genes overlap, only 13% of morning-phased and 22% of evening-phased genes had both H3K4me3 and H3K9ac peaks, suggesting specific roles of different histone modifications in diurnal gene expression. Conclusions Circadian clock genes promote diurnal regulation of SDG2 and JMJ14 expression, which in turn regulate rhythmic histone modification dynamics for the clock and its output genes. This reciprocal regulatory module between chromatin modifiers and circadian clock oscillators orchestrates diurnal gene expression that governs plant growth and development. Electronic supplementary material The online version of this article (10.1186/s13059-019-1777-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tien-Yu Huang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Helen H Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Atsumi Ando
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Misook Ha
- Samsung Advanced Institute of Technology, Samsung Electronics Corporation, Suwon, 443-803, South Korea.
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA. .,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA. .,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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22
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Huang S, Zhang A, Jin JB, Zhao B, Wang TJ, Wu Y, Wang S, Liu Y, Wang J, Guo P, Ahmad R, Liu B, Xu ZY. Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress response. THE NEW PHYTOLOGIST 2019; 223:1372-1387. [PMID: 31038749 DOI: 10.1111/nph.15874] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Under dehydration in plants, antagonistic activities of histone 3 lysine 4 (H3K4) methyltransferase and histone demethylase maintain a dynamic and homeostatic state of gene expression by orientating transcriptional reprogramming toward growth or stress tolerance. However, the histone demethylase that specifically controls histone methylation homeostasis under dehydration stress remains unknown. Here, we document that a histone demethylase, JMJ17, belonging to the KDM5/JARID1 family, plays crucial roles in response to dehydration stress and abscisic acid (ABA) in Arabidopsis thaliana. jmj17 loss-of-function mutants displayed dehydration stress tolerance and ABA hypersensitivity in terms of stomatal closure. JMJ17 specifically demethylated H3K4me1/2/3 via conserved iron-binding amino acids in vitro and in vivo. Moreover, H3K4 demethylase activity of JMJ17 was required for dehydration stress response. Systematic combination of genome-wide chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) analyses revealed that a loss-of-function mutation in JMJ17 caused an ectopic increase in genome-wide H3K4me3 levels and activated a plethora of dehydration stress-responsive genes. Importantly, JMJ17 bound directly to the chromatin of OPEN STOMATA 1 (OST1) and demethylated H3K4me3 for the regulation of OST1 mRNA abundance, thereby modulating the dehydration stress response. Our results demonstrate a new function of a histone demethylase under dehydration stress in plants.
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Affiliation(s)
- Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jing Bo Jin
- Key Laboratory of Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Bo Zhao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yifan Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Rafiq Ahmad
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - 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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23
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Fiorucci AS, Bourbousse C, Concia L, Rougée M, Deton-Cabanillas AF, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M, Barneche F. Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. Genome Biol 2019; 20:100. [PMID: 31113491 PMCID: PMC6528313 DOI: 10.1186/s13059-019-1705-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022] Open
Abstract
Background The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Saccharomyces cerevisiae, where a single SET1 protein catalyzes H3K4me3 as part of COMPlex of proteins ASsociated with Set1 (COMPASS), in Arabidopsis thaliana, this activity involves multiple histone methyltransferases. Among these, the plant-specific SET DOMAIN GROUP 2 (SDG2) has a prominent role. Results We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. We show that S2Lb co-purifies with the AtCOMPASS core subunit WDR5, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. However, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2, or H3K4me3, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Conclusions Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been co-opted by the plant-specific SDG2 histone methyltransferase and mediates H3K4me3 deposition through an H2B monoubiquitination-independent pathway in Arabidopsis. Electronic supplementary material The online version of this article (10.1186/s13059-019-1705-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne-Sophie Fiorucci
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.,Present address: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Martin Rougée
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Gérald Zabulon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Elodie Layat
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Soon Kap Kim
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Nicole Chaumont
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - Bérangère Lombard
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - David Stroebel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Sophie Lemoine
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Ammara Mohammad
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Corinne Blugeon
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.
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24
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Roy D, Chakrabarty J, Mallik R, Chaudhuri S. Rice Trithorax factor ULTRAPETALA 1 (OsULT1) specifically binds to “GAGAG” sequence motif present in Polycomb response elements. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:582-597. [DOI: 10.1016/j.bbagrm.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 02/07/2023]
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25
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Tian Y, Zheng H, Zhang F, Wang S, Ji X, Xu C, He Y, Ding Y. PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR. SCIENCE ADVANCES 2019; 5:eaau7246. [PMID: 31032401 PMCID: PMC6482009 DOI: 10.1126/sciadv.aau7246] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 03/14/2019] [Indexed: 05/18/2023]
Abstract
The cold-induced antisense transcript COOLAIR represses FLOWERING LOCUS C (FLC) transcription with increased H3K27me3 and decreased H3K36me3 levels in response to cold temperatures. However, the molecular connection between COOLAIR and histone modification factors in the absence of cold treatment remains unclear. We report that the RNA binding protein FCA interacts with the PRC2 subunit CURLY LEAF (CLF) and binds nascent COOLAIR transcripts to allow deposition of H3K27me3 at FLC. Loss of COOLAIR function results in a reduction in FCA and CLF enrichment, which, in turn, decreases H3K27me3 levels at FLC. The Arabidopsis protein phosphatase SSU72 physically interacts with the RRM1 motif of FCA to antagonize FCA binding with COOLAIR. Mutations in SSU72 caused early flowering, reduced FLC transcription, increased CLF enrichment and H3K27me3, and enhanced affinity between FCA and COOLAIR. Our results suggest that FCA binding of COOLAIR and SSU72 is critical for PRC2 enrichment and H3K27me3 deposition in Arabidopsis.
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Affiliation(s)
- Yongke Tian
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, and Division of Molecular Cell Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Anhui 230027, China
| | - Han Zheng
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, and Division of Molecular Cell Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Anhui 230027, China
| | - Fei Zhang
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, and Division of Molecular Cell Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Anhui 230027, China
| | - Shiliang Wang
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, and Division of Molecular Cell Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Anhui 230027, China
| | - Xiaoru Ji
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, and Division of Molecular Cell Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Anhui 230027, China
| | - Chao Xu
- School of Life Sciences, University of Science and Technology of China, and Division of Molecular Cell Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Anhui 230027, China
| | - Yuehui He
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201602, China
- Shanghai Chenshan Plant Science Research Center, CAS, Shanghai 201602, China
| | - Yong Ding
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, and Division of Molecular Cell Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Anhui 230027, China
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26
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Avramova Z. Defence-related priming and responses to recurring drought: Two manifestations of plant transcriptional memory mediated by the ABA and JA signalling pathways. PLANT, CELL & ENVIRONMENT 2019; 42:983-997. [PMID: 30299553 DOI: 10.1111/pce.13458] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 09/26/2018] [Accepted: 10/02/2018] [Indexed: 05/20/2023]
Abstract
Collective evidence from agricultural practices and from scientific research has demonstrated that plants can alter their phenotypic responses to repeated biotic and abiotic stresses or their elicitors. A coordinated reaction at the organismal, cellular, and genome levels has suggested that plants can "remember" an earlier stress and modify their future responses, accordingly. Stress memory may increase a plant's survival chances by improving its tolerance/avoidance abilities and may provide a mechanism for acclimation and adaptation. Understanding the mechanisms that regulate plant stress memory is not only an intellectually challenging topic but has important implications for agricultural practices as well. Here, I focus exclusively on specific aspects of the transcription memory in response to recurring dehydration stresses and the memory-type responses to insect damage in a process known as "priming." The questions discussed are (a) whether/how the two memory phenomena are connected at the level of transcriptional regulation; (b) how differential transcription is achieved mechanistically under a repeated stress; and (c) whether similar molecular and/or epigenetic mechanisms are involved. Possible biological relevance of transcriptional stress memory and its preservation in plant evolution are also discussed.
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Affiliation(s)
- Zoya Avramova
- School of Biological Sciences, UNL, Lincoln, Nebraska
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27
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Bedi S, Nag Chaudhuri R. Transcription factor
ABI
3 auto‐activates its own expression during dehydration stress response. FEBS Lett 2018; 592:2594-2611. [DOI: 10.1002/1873-3468.13194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Sonia Bedi
- Department of Biotechnology St. Xavier's College Kolkata India
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28
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Jiang P, Wang S, Ikram AU, Xu Z, Jiang H, Cheng B, Ding Y. SDG721 and SDG705 are required for rice growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:530-535. [PMID: 29473711 DOI: 10.1111/jipb.12644] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 02/22/2018] [Indexed: 05/27/2023]
Abstract
H3K4me3 plays important roles in development, transcription, and environmental responses. Here, we report that SDG721 (SET-domain group protein 721) and SDG705 are involved in regulating rice development. SDG721 and SDG705 encode TRITHORAX-like proteins, which appear to modulate H3K4 methylation levels. Loss of SDG721 and SDG705 function resulted in GA-deficient phenotypes, including semi-dwarfism, reduced cell length, and reduced panicle branching. The transcripts levels and H3K4me3 levels of GA biosynthesis genes and GA signaling pathway genes were downregulated in the sdg721 sdg705 plants. Together, these results suggest that SDG721 and SDG705 regulate H3K4 methylation, which is crucial for plant development in rice.
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Affiliation(s)
- Pengfei Jiang
- National Engineering Laboratory of Crop Stress Resistance/ Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Shiliang Wang
- National Engineering Laboratory of Crop Stress Resistance/ Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Aziz Ul Ikram
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Zuntao Xu
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Haiyang Jiang
- National Engineering Laboratory of Crop Stress Resistance/ Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance/ Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yong Ding
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science & Technology of China, Hefei 230027, China
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29
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Jiang P, Wang S, Zheng H, Li H, Zhang F, Su Y, Xu Z, Lin H, Qian Q, Ding Y. SIP1 participates in regulation of flowering time in rice by recruiting OsTrx1 to Ehd1. THE NEW PHYTOLOGIST 2018; 219:422-435. [PMID: 29611871 PMCID: PMC6001661 DOI: 10.1111/nph.15122] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/20/2018] [Indexed: 05/12/2023]
Abstract
Flowering time (heading date) in rice (Oryza sativa) is an important agronomic trait that determines yield. The levels of histone H3 lysine 4 trimethylation (H3K4me3) modulated by TRITHORAX-like proteins regulate gene transcription, flowering time and environmental stress responses. However, plant TRITHORAX-like proteins have no known DNA-binding domain, and therefore the mechanism that gives sequence specificity to these proteins remains unclear. Here, we show that the rice TRITHORAX-like protein OsTrx1 is recruited to its target, Early heading date 1 (Ehd1), by the C2H2 zinc finger protein SDG723/OsTrx1/OsSET33 Interaction Protein 1 (SIP1). SIP1 binds to the promoter of Ehd1 and interacts with OsTrx1. Mutations in SIP1 led to a late heading date under long-day and short-day conditions. Defects in OsTrx1 or SIP1 led to reduced H3K4me3 levels at Ehd1, thus reducing Ehd1 expression. Together, our results show that the transcription factor SIP1 interacts with OxTrx1, allowing OsTrx1 to specifically target Ehd1, altering H3K4me3 levels, increasing Ehd1 expression and thereby promoting flowering.
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Affiliation(s)
- Pengfei Jiang
- CAS Center for Excellence in Molecular Plant SciencesSchool of Life SciencesUniversity of Science & Technology of ChinaHefeiAnhui230027China
- School of Life SciencesAnhui Agricultural UniversityHefeiAnhui230036China
| | - Shiliang Wang
- CAS Center for Excellence in Molecular Plant SciencesSchool of Life SciencesUniversity of Science & Technology of ChinaHefeiAnhui230027China
- School of Life SciencesAnhui Agricultural UniversityHefeiAnhui230036China
| | - Han Zheng
- CAS Center for Excellence in Molecular Plant SciencesSchool of Life SciencesUniversity of Science & Technology of ChinaHefeiAnhui230027China
| | - Hao Li
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefei230031China
| | - Fei Zhang
- CAS Center for Excellence in Molecular Plant SciencesSchool of Life SciencesUniversity of Science & Technology of ChinaHefeiAnhui230027China
| | - Yanhua Su
- CAS Center for Excellence in Molecular Plant SciencesSchool of Life SciencesUniversity of Science & Technology of ChinaHefeiAnhui230027China
| | - Zuntao Xu
- CAS Center for Excellence in Molecular Plant SciencesSchool of Life SciencesUniversity of Science & Technology of ChinaHefeiAnhui230027China
| | - Haiyan Lin
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China
| | - Qian Qian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China
| | - Yong Ding
- CAS Center for Excellence in Molecular Plant SciencesSchool of Life SciencesUniversity of Science & Technology of ChinaHefeiAnhui230027China
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30
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Xu F, Kuo T, Rosli Y, Liu MS, Wu L, Chen LFO, Fletcher JC, Sung ZR, Pu L. Trithorax Group Proteins Act Together with a Polycomb Group Protein to Maintain Chromatin Integrity for Epigenetic Silencing during Seed Germination in Arabidopsis. MOLECULAR PLANT 2018; 11:659-677. [PMID: 29428247 DOI: 10.1016/j.molp.2018.01.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 01/01/2018] [Accepted: 01/29/2018] [Indexed: 05/02/2023]
Abstract
Polycomb group (PcG) and trithorax group (trxG) proteins have been shown to act antagonistically to epigenetically regulate gene expression in eukaryotes. The trxG proteins counteract PcG-mediated floral repression in Arabidopsis, but their roles in other developmental processes are poorly understood. We investigated the interactions between the trxG genes, ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1) and ULTRAPETALA1 (ULT1), and the PcG gene EMBRYONIC FLOWER 1 (EMF1) during early development. Unexpectedly, we found that mutations in the trxG genes failed to rescue the early-flowering phenotype of emf1 mutants. Instead, emf1 atx1 ult1 seedlings showed a novel swollen root phenotype and massive deregulation of gene expression. Greater ectopic expression of seed master regulatory genes in emf1 atx1 ult1 triple than in emf1 single mutants indicates that PcG and trxG factors together repress seed gene expression after germination. Furthermore, we found that the widespread gene derepression is associated with reduced levels of H3K27me3, an epigenetic repressive mark of gene expression, and with globally altered chromatin organization. EMF1, ATX1, and ULT1 are able to bind the chromatin of seed genes and ULT1 can physically interact with ATX1 and EMF1, suggesting that the trxG and EMF1 proteins directly associate at target gene loci for EMF1-mediated gene silencing. Thus, while ATX1, ULT1, and EMF1 interact antagonistically to regulate flowering, they work together to maintain chromatin integrity and prevent precocious seed gene expression after germination.
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Affiliation(s)
- Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tony Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, China
| | - Yenny Rosli
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Mao-Sen Liu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, China
| | - Limin Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Long-Fang Oliver Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, China
| | - Jennifer C Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Zinmay Renee Sung
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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Jiang P, Wang S, Jiang H, Cheng B, Wu K, Ding Y. The COMPASS-Like Complex Promotes Flowering and Panicle Branching in Rice. PLANT PHYSIOLOGY 2018; 176:2761-2771. [PMID: 29440594 PMCID: PMC5884598 DOI: 10.1104/pp.17.01749] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/05/2018] [Indexed: 05/21/2023]
Abstract
Flowering time (heading date) and panicle branch number are important agronomic traits that determine yield in rice (Oryza sativa). The activation of flowering requires histone methylation, but the roles of trimethylation of Lys 4 of histone 3 (H3K4me3) in modulating heading date and panicle development are unclear. Here, we showed that the COMPASS-like complex promotes flowering and panicle branching. The rice (Oryza sativa) WD40 protein OsWDR5a interacts with the TRITHORAX-like protein OsTrx1/SET domain group protein 723 (SDG723) to form the core components of the COMPASS-like complex. Plants in which OsWDR5a or OsTrx1 expression was decreased by RNA interference produced fewer secondary branches and less grain and exhibited a delayed heading date under long-day and short-day conditions, whereas loss of OsWDR5a function resulted in embryo lethality. OsWDR5a binds to Early heading date 1 to regulate its H3K4me3 and expression levels. Together, our results show that the COMPASS-like complex promotes flowering and panicle development and suggest that modulation of H3K4me3 levels by the COMPASS-like complex is critical for rice development.
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Affiliation(s)
- Pengfei Jiang
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China 230027
- National Engineering Laboratory of Crop Stress Resistance/ Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China 230036
| | - Shiliang Wang
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China 230027
- National Engineering Laboratory of Crop Stress Resistance/ Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China 230036
| | - Haiyang Jiang
- National Engineering Laboratory of Crop Stress Resistance/ Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China 230036
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance/ Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China 230036
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan 10617
| | - Yong Ding
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China 230027
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Ma Y, Gil S, Grasser KD, Mas P. Targeted Recruitment of the Basal Transcriptional Machinery by LNK Clock Components Controls the Circadian Rhythms of Nascent RNAs in Arabidopsis. THE PLANT CELL 2018; 30:907-924. [PMID: 29618629 PMCID: PMC5973845 DOI: 10.1105/tpc.18.00052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/02/2018] [Accepted: 04/02/2018] [Indexed: 05/21/2023]
Abstract
The rhythms of steady-state mRNA expression pervade nearly all circadian systems. However, the mechanisms behind the rhythmic transcriptional synthesis and its correlation with circadian expression remain fully unexplored, particularly in plants. Here, we discovered a multifunctional protein complex that orchestrates the rhythms of transcriptional activity in Arabidopsis thaliana The expression of the circadian oscillator genes TIMING OF CAB EXPRESSION1/PSEUDO-RESPONSE REGULATOR1 and PSEUDO-RESPONSE REGULATOR5 initially relies on the modular function of the clock-related factor REVEILLE8: its MYB domain provides the DNA binding specificity, while its LCL domain recruits the clock components, NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED proteins (LNKs), to target promoters. LNKs, in turn, specifically interact with RNA Polymerase II and the transcript elongation FACT complex to rhythmically co-occupy the target loci. The functional interaction of these components is central for chromatin status, transcript initiation, and elongation as well as for proper rhythms in nascent RNAs. Thus, our findings explain how genome readout of environmental information ultimately results in rhythmic changes of gene expression.
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Affiliation(s)
- Yuan Ma
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Sergio Gil
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Klaus D Grasser
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Paloma Mas
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain
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Liu Y, Zhang A, Yin H, Meng Q, Yu X, Huang S, Wang J, Ahmad R, Liu B, Xu ZY. Trithorax-group proteins ARABIDOPSIS TRITHORAX4 (ATX4) and ATX5 function in abscisic acid and dehydration stress responses. THE NEW PHYTOLOGIST 2018; 217:1582-1597. [PMID: 29250818 DOI: 10.1111/nph.14933] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/02/2017] [Indexed: 05/10/2023]
Abstract
Trithorax-group proteins (TrxGs) play essential regulatory roles in chromatin modification to activate transcription. Although TrxGs have been shown to be extensively involved in the activation of developmental genes, how the specific TrxGs function in the dehydration and abscisic acid (ABA)-mediated modulation of downstream gene expression remains unknown. Here, we report that two evolutionarily conserved Arabidopsis thaliana TrxGs, ARABIDOPSIS TRITHORAX4 (ATX4) and ATX5, play essential roles in the drought stress response. atx4 and atx5 single loss-of-function mutants showed drought stress-tolerant and ABA-hypersensitive phenotypes during seed germination and seedling development, while the atx4 atx5 double mutant displayed further exacerbation of the phenotypes. Genome-wide RNA-sequencing analyses showed that ATX4 and ATX5 regulate the expression of genes functioning in dehydration stress. Intriguingly, ABA-HYPERSENSITIVE GERMINATION 3 (AHG3), an essential negative regulator of ABA signaling, acts genetically downstream of ATX4 and ATX5 in response to ABA. ATX4 and ATX5 directly bind to the AHG3 locus and trimethylate histone H3 of Lys 4 (H3K4). Moreover, ATX4 and ATX5 occupancies at AHG3 are dramatically increased under ABA treatment, and are also essential for RNA polymerase II (RNAPII) occupancies. Our findings reveal novel molecular functions of A. thaliana TrxGs in dehydration stress and ABA responses.
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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
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Hao Yin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Qingxiang Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Rafiq Ahmad
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - 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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Lopez SJ, Dunaway K, Islam MS, Mordaunt C, Vogel Ciernia A, Meguro-Horike M, Horike SI, Segal DJ, LaSalle JM. UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons. Epigenetics 2017; 12:982-990. [PMID: 28925810 PMCID: PMC5788436 DOI: 10.1080/15592294.2017.1376151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenotypes is a complex, multilayered process involving both genetics and epigenetics. Parent-of-origin effects of deletion and duplication of the 15q11-q13 locus leading to Angelman, Prader-Willi, and Dup15q syndromes are due to imprinted genes, including UBE3A, which is maternally expressed exclusively in neurons. UBE3A encodes a ubiquitin E3 ligase protein with multiple downstream targets, including RING1B, which in turn monoubiquitinates histone variant H2A.Z. To understand the impact of neuronal UBE3A levels on epigenome-wide marks of DNA methylation, histone variant H2A.Z positioning, active H3K4me3 promoter marks, and gene expression, we took a multi-layered genomics approach. We performed an siRNA knockdown of UBE3A in two human neuroblastoma cell lines, including parental SH-SY5Y and the SH(15M) model of Dup15q. Genes differentially methylated across cells with differing UBE3A levels were enriched for functions in gene regulation, DNA binding, and brain morphology. Importantly, we found that altering UBE3A levels had a profound epigenetic effect on the methylation levels of up to half of known imprinted genes. Genes with differential H2A.Z peaks in SH(15M) compared to SH-SY5Y were enriched for ubiquitin and protease functions and associated with autism, hypoactivity, and energy expenditure. Together, these results support a genome-wide epigenetic consequence of altered UBE3A levels in neurons and suggest that UBE3A regulates an imprinted gene network involving DNA methylation patterning and H2A.Z deposition.
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Affiliation(s)
- S Jesse Lopez
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
| | - Keith Dunaway
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
| | - M Saharul Islam
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Charles Mordaunt
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Annie Vogel Ciernia
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Makiko Meguro-Horike
- f Advanced Science Research Center , Kanazawa University , 13-1 Takaramachi, Kanazawa , Ishikawa , Japan
| | - Shin-Ichi Horike
- f Advanced Science Research Center , Kanazawa University , 13-1 Takaramachi, Kanazawa , Ishikawa , Japan
| | - David J Segal
- b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA.,e Biochemistry and Molecular Medicine , University of California , Davis , CA , USA
| | - Janine M LaSalle
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
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Chen LQ, Luo JH, Cui ZH, Xue M, Wang L, Zhang XY, Pawlowski WP, He Y. ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development. PLANT PHYSIOLOGY 2017; 174:1795-1806. [PMID: 28550207 PMCID: PMC5490889 DOI: 10.1104/pp.16.01944] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/23/2017] [Indexed: 05/19/2023]
Abstract
Methylation of Lys residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis (Arabidopsis thaliana) encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related proteins. Here, we examined three until-now-unexplored ATX proteins, ATX3, ATX4, and ATX5. We found that they exhibit similar domain structures and expression patterns and are redundantly required for vegetative and reproductive development. Concurrent disruption of the ATX3, ATX4, and ATX5 genes caused marked reduction in H3K4me2 and H3K4me3 levels genome-wide and resulted in thousands of genes expressed ectopically. Furthermore, atx3/atx4/atx5 triple mutants resulted in exaggerated phenotypes when combined with the atx2 mutant but not with atx1 Together, we conclude that ATX3, ATX4, and ATX5 are redundantly required for H3K4 di- and trimethylation at thousands of sites located across the genome, and genomic features associated with targeted regions are different from the ATXR3/SDG2-controlled sites in Arabidopsis.
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Affiliation(s)
- Li-Qun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100083, China
| | - Jin-Hong Luo
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100083, China
| | - Zhen-Hai Cui
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100083, China
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ming Xue
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100083, China
| | - Li Wang
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts 02142
| | - Xiao-Yu Zhang
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | | | - Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100083, China
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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36
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Berr A, Zhang X, Shen WH. [Reciprocity between active transcription and histone methylation]. Biol Aujourdhui 2017; 210:269-282. [PMID: 28327284 DOI: 10.1051/jbio/2017004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Indexed: 01/08/2023]
Abstract
In the nucleus of eukaryotic cells, the chromatin states dictated by the different combinations of histone post-translational modifications, such as the methylation of lysine residues, are an integral part of the multitude of epigenomes involved in the fine tuning of all genome functions, and in particular transcription. Over the last decade, an increasing number of factors have been identified as regulators involved in the establishment, reading or erasure of histone methylations. Their characterization in model organisms such as Arabidopsis has thus unraveled their fundamental roles in the control and regulation of essential developmental processes such as the floral transition, cell differentiation, gametogenesis, and/or the response/adaptation of plants to environmental stresses. In this review, we will focus on the methylation of histones functioning as a mark of activate transcription and we will try to highlight, based on recent findings, the more or less direct links between this mark and gene expression. Thus, we will discuss the different mechanisms allowing the dynamics and the integration of the chromatin states resulting from the different histone methylations in connection with the transcriptional machinery of the RNA polymerase II.
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Lu C, Tian Y, Wang S, Su Y, Mao T, Huang T, Chen Q, Xu Z, Ding Y. Phosphorylation of SPT5 by CDKD;2 Is Required for VIP5 Recruitment and Normal Flowering in Arabidopsis thaliana. THE PLANT CELL 2017; 29:277-291. [PMID: 28188267 PMCID: PMC5354186 DOI: 10.1105/tpc.16.00568] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 01/10/2017] [Accepted: 02/09/2017] [Indexed: 05/10/2023]
Abstract
The elongation factor suppressor of Ty 5 homolog (Spt5) is a regulator of transcription and histone methylation. In humans, phosphorylation of SPT5 by P-TEFb, a protein kinase composed of Cyclin-dependent kinase 9 (CDK9) and cyclin T, interacts with the RNA polymerase II-associated factor1 (PAF1) complex. However, the mechanism of SPT5 phosphorylation is not well understood in plants. Here, we examine the function of SPT5 in Arabidopsis thaliana and find that spt5 mutant flowers early under long-day and short-day conditions. SPT5 interacts with the CDK-activating kinase 4 (CAK4; CDKD;2) and is specifically phosphorylated by CDKD;2 at threonines. The phosphorylated SPT5 binds VERNALIZATION INDEPENDENCE5 (VIP5), a subunit of the PAF1 complex. Genetic analysis showed that VIP5 acts downstream of SPT5 and CDKD;2 Loss of SPT5 or CDKD;2 function results in early flowering because of decreased amounts of FLOWERING LOCUS C (FLC) transcript. Importantly, CDKD;2 and SPT5 are required for the deposition of VIP5 and the enhancement of trimethylation of histone 3 lysine 4 in the chromatin of the FLC locus. Together, our results provide insight into the mechanism by which the Arabidopsis elongation factor SPT5 recruits the PAF1 complex via the posttranslational modification of proteins and suggest that the phosphorylation of SPT5 by CDKD;2 enables it to recruit VIP5 to regulate chromatin and transcription in Arabidopsis.
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Affiliation(s)
- Chengyuan Lu
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Yongke Tian
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Shiliang Wang
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Yanhua Su
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Ting Mao
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Tongtong Huang
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Qingqing Chen
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Zuntao Xu
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Yong Ding
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
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Peng M, Ying P, Liu X, Li C, Xia R, Li J, Zhao M. Genome-Wide Identification of Histone Modifiers and Their Expression Patterns during Fruit Abscission in Litchi. FRONTIERS IN PLANT SCIENCE 2017; 8:639. [PMID: 28496451 PMCID: PMC5406457 DOI: 10.3389/fpls.2017.00639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 04/10/2017] [Indexed: 05/07/2023]
Abstract
Modifications to histones, including acetylation and methylation processes, play crucial roles in the regulation of gene expression in plant development as well as in stress responses. However, limited information on the enzymes catalyzing histone acetylation and methylation in non-model plants is currently available. In this study, several histone modifier (HM) types, including six histone acetyltransferases (HATs), 11 histone deacetylases (HDACs), 48 histone methyltransferases (HMTs), and 22 histone demethylases (HDMs), are identified in litchi (Litchi chinensis Sonn. cv. Feizixiao) based on similarities in their sequences to homologs in Arabidopsis (A. thaliana), tomato (Solanum lycopersicum), and rice (Oryza sativa). Phylogenetic analyses reveal that HM enzymes can be grouped into four HAT, two HDAC, two HMT, and two HDM subfamilies, respectively, while further expression profile analyses demonstrate that 17 HMs were significantly altered during fruit abscission in two field treatments. Analyses reveal that these genes exhibit four distinct patterns of expression in response to fruit abscission, while an in vitro assay was used to confirm the HDAC activity of LcHDA2, LcHDA6, and LcSRT2. Our findings are the first in-depth analysis of HMs in the litchi genome, and imply that some are likely to play important roles in fruit abscission in this commercially important plant.
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Affiliation(s)
- Manjun Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, China Litchi Research Center, South China Agricultural UniversityGuangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Peiyuan Ying
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, China Litchi Research Center, South China Agricultural UniversityGuangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Xuncheng Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Caiqin Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, China Litchi Research Center, South China Agricultural UniversityGuangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, China Litchi Research Center, South China Agricultural UniversityGuangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, China Litchi Research Center, South China Agricultural UniversityGuangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural UniversityGuangzhou, China
- *Correspondence: Jianguo Li
| | - Minglei Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, China Litchi Research Center, South China Agricultural UniversityGuangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural UniversityGuangzhou, China
- Minglei Zhao
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Fletcher JC. State of the Art: trxG Factor Regulation of Post-embryonic Plant Development. FRONTIERS IN PLANT SCIENCE 2017; 8:1925. [PMID: 29184559 PMCID: PMC5694493 DOI: 10.3389/fpls.2017.01925] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/24/2017] [Indexed: 05/07/2023]
Abstract
Multicellular organisms rely on the precise and consistent regulation of gene expression to direct their development in tissue- and cell-type specific patterns. This regulatory activity involves arrays of DNA-binding transcription factors and epigenetic factors that modify chromatin structure. Among the chromatin modifiers, trithorax (trxG) and Polycomb (PcG) group proteins play important roles in orchestrating the stable activation and repression of gene expression, respectively. These proteins have generally antagonistic functions in maintaining cell and tissue homeostasis as well as in mediating widespread transcriptional reprogramming during developmental transitions. Plants utilize multiple trxG factors to regulate gene transcription as they modulate their development in response to both endogenous and environmental cues. Here, I will discuss the roles of trxG factors and their associated proteins in post-embryonic plant development.
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Affiliation(s)
- Jennifer C. Fletcher
- Plant Gene Expression Center, United States Department of Agriculture – Agricultural Research Service, Albany, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: Jennifer C. Fletcher,
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Liu N, Avramova Z. Molecular mechanism of the priming by jasmonic acid of specific dehydration stress response genes in Arabidopsis. Epigenetics Chromatin 2016; 9:8. [PMID: 26918031 PMCID: PMC4766709 DOI: 10.1186/s13072-016-0057-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant genes that provide a different response to a similar dehydration stress illustrate the concept of transcriptional 'dehydration stress memory'. Pre-exposing a plant to a biotic stress or a stress-signaling hormone may increase transcription from response genes in a future stress, a phenomenon known as 'gene priming'. Although known that primed transcription is preceded by accumulation of H3K4me3 marks at primed genes, what mechanism provides for their appearance before the transcription was unclear. How augmented transcription is achieved, whether/how the two memory phenomena are connected at the transcriptional level, and whether similar molecular and/or epigenetic mechanisms regulate them are fundamental questions about the molecular mechanisms regulating gene expression. RESULTS Although the stress hormone jasmonic acid (JA) was unable to induce transcription of tested dehydration stress response genes, it strongly potentiated transcription from specific ABA-dependent 'memory' genes. We elucidate the molecular mechanism causing their priming, demonstrate that stalled RNA polymerase II and H3K4me3 accumulate as epigenetic marks at the JA-primed ABA-dependent genes before actual transcription, and describe how these events occur mechanistically. The transcription factor MYC2 binds to the genes in response to both dehydration stress and to JA and determines the specificity of the priming. The MEDIATOR subunit MED25 links JA-priming with dehydration stress response pathways at the transcriptional level. Possible biological relevance of primed enhanced transcription from the specific memory genes is discussed. CONCLUSIONS The biotic stress hormone JA potentiated transcription from a specific subset of ABA-response genes, revealing a novel aspect of the JA- and ABA-signaling pathways' interactions. H3K4me3 functions as an epigenetic mark at JA-primed dehydration stress response genes before transcription. We emphasize that histone and epigenetic marks are not synonymous and argue that distinguishing between them is important for understanding the role of chromatin marks in genes' transcriptional performance. JA-priming, specifically of dehydration stress memory genes encoding cell/membrane protective functions, suggests it is an adaptational response to two different environmental stresses.
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Affiliation(s)
- Ning Liu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Zoya Avramova
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
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Moreau F, Thévenon E, Blanvillain R, Lopez-Vidriero I, Franco-Zorrilla JM, Dumas R, Parcy F, Morel P, Trehin C, Carles CC. The Myb-domain protein ULTRAPETALA1 INTERACTING FACTOR 1 controls floral meristem activities in Arabidopsis. Development 2016; 143:1108-19. [PMID: 26903506 DOI: 10.1242/dev.127365] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 02/15/2016] [Indexed: 11/20/2022]
Abstract
Higher plants continuously and iteratively produce new above-ground organs in the form of leaves, stems and flowers. These organs arise from shoot apical meristems whose homeostasis depends on coordination between self-renewal of stem cells and their differentiation into organ founder cells. This coordination is stringently controlled by the central transcription factor WUSCHEL (WUS), which is both necessary and sufficient for stem cell specification in Arabidopsis thaliana ULTRAPETALA1 (ULT1) was previously identified as a plant-specific, negative regulator of WUS expression. However, molecular mechanisms underlying this regulation remain unknown. ULT1 protein contains a SAND putative DNA-binding domain and a B-box, previously proposed as a protein interaction domain in eukaryotes. Here, we characterise a novel partner of ULT1, named ULT1 INTERACTING FACTOR 1 (UIF1), which contains a Myb domain and an EAR motif. UIF1 and ULT1 function in the same pathway for regulation of organ number in the flower. Moreover, UIF1 displays DNA-binding activity and specifically binds to WUS regulatory elements. We thus provide genetic and molecular evidence that UIF1 and ULT1 work together in floral meristem homeostasis, probably by direct repression of WUS expression.
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Affiliation(s)
- Fanny Moreau
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble 38054, France CNRS, LPCV, UMR 5168, Grenoble 38054, France CEA, Direction des Sciences du Vivant, BIG, LPCV, Grenoble 38054, France INRA, LPCV, Grenoble 38054, France
| | - Emmanuel Thévenon
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble 38054, France CNRS, LPCV, UMR 5168, Grenoble 38054, France CEA, Direction des Sciences du Vivant, BIG, LPCV, Grenoble 38054, France INRA, LPCV, Grenoble 38054, France
| | - Robert Blanvillain
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble 38054, France CNRS, LPCV, UMR 5168, Grenoble 38054, France CEA, Direction des Sciences du Vivant, BIG, LPCV, Grenoble 38054, France INRA, LPCV, Grenoble 38054, France
| | - Irene Lopez-Vidriero
- Genomics Unit, Centro Nacional de Biotecnologia CNB- CSIC, Darwin 3, Madrid 28049, Spain
| | | | - Renaud Dumas
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble 38054, France CNRS, LPCV, UMR 5168, Grenoble 38054, France CEA, Direction des Sciences du Vivant, BIG, LPCV, Grenoble 38054, France INRA, LPCV, Grenoble 38054, France
| | - François Parcy
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble 38054, France CNRS, LPCV, UMR 5168, Grenoble 38054, France CEA, Direction des Sciences du Vivant, BIG, LPCV, Grenoble 38054, France INRA, LPCV, Grenoble 38054, France
| | - Patrice Morel
- Laboratoire de Reproduction et Développement des Plantes, Université Lyon1, CNRS, INRA, ENS, Lyon cedex 07 69347, France
| | - Christophe Trehin
- Laboratoire de Reproduction et Développement des Plantes, Université Lyon1, CNRS, INRA, ENS, Lyon cedex 07 69347, France
| | - Cristel C Carles
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble 38054, France CNRS, LPCV, UMR 5168, Grenoble 38054, France CEA, Direction des Sciences du Vivant, BIG, LPCV, Grenoble 38054, France INRA, LPCV, Grenoble 38054, France
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43
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Avramova Z. Transcriptional 'memory' of a stress: transient chromatin and memory (epigenetic) marks at stress-response genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:149-59. [PMID: 25788029 DOI: 10.1111/tpj.12832] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 05/17/2023]
Abstract
Drought, salinity, extreme temperature variations, pathogen and herbivory attacks are recurring environmental stresses experienced by plants throughout their life. To survive repeated stresses, plants provide responses that may be different from their response during the first encounter with the stress. A different response to a similar stress represents the concept of 'stress memory'. A coordinated reaction at the organismal, cellular and gene/genome levels is thought to increase survival chances by improving the plant's tolerance/avoidance abilities. Ultimately, stress memory may provide a mechanism for acclimation and adaptation. At the molecular level, the concept of stress memory indicates that the mechanisms responsible for memory-type transcription during repeated stresses are not based on repetitive activation of the same response pathways activated by the first stress. Some recent advances in the search for transcription 'memory factors' are discussed with an emphasis on super-induced dehydration stress memory response genes in Arabidopsis.
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Affiliation(s)
- Zoya Avramova
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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44
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PcG and trxG in plants - friends or foes. Trends Genet 2015; 31:252-62. [PMID: 25858128 DOI: 10.1016/j.tig.2015.03.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 01/07/2023]
Abstract
The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals.
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Transcription factor interaction with COMPASS-like complex regulates histone H3K4 trimethylation for specific gene expression in plants. Proc Natl Acad Sci U S A 2015; 112:2900-5. [PMID: 25730865 DOI: 10.1073/pnas.1419703112] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accumulation of unfolded or misfolded proteins causes endoplasmic reticulum (ER) stress, which activates a set of ER membrane-associated transcription factors for protein homeostasis regulation. Previous genome-wide chromatin immunoprecipitation analysis shows a strong correlation between histone H3K4 trimethylation (H3K4me3) and active gene expression. However, how the histone modification complex is specifically and timely recruited to the active promoters remains unknown. Using ER stress responsive gene expression as a model system, we demonstrate that sequence-specific transcription factors interact with COMPASS-like components and affect H3K4me3 formation at specific target sites in Arabidopsis. Gene profiling analysis reveals that membrane-associated basic leucine zipper (bZIP) transcription factors bZIP28 and bZIP60 regulate most of the ER stress responsive genes. Loss-of-functions of bZIP28 and bZIP60 impair the occupancy of H3K4me3 on promoter regions of ER stress responsive genes. Further, in vitro pull-down assays and in vivo bimolecular fluorescence complementation (BiFC) experiments show that bZIP28 and bZIP60 interact with Ash2 and WDR5a, both of which are core COMPASS-like components. Knockdown expression of either Ash2 or WDR5a decreased the expression of several ER stress responsive genes. The COMPASS-like complex is known to interact with histone methyltransferase to facilitate preinitiation complex (PIC) assembly and generate H3K4me3 during transcription elongation. Thus, our data shows that the ER stress stimulus causes the formation of PIC and deposition of H3K4me3 mark at specific promoters through the interaction between transcription factor and COMPASS-like components.
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46
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Engelhorn J, Moreau F, Fletcher JC, Carles CC. ULTRAPETALA1 and LEAFY pathways function independently in specifying identity and determinacy at the Arabidopsis floral meristem. ANNALS OF BOTANY 2014; 114:1497-505. [PMID: 25288633 PMCID: PMC4204788 DOI: 10.1093/aob/mcu185] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/14/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The morphological variability of the flower in angiosperms, combined with its relatively simple structure, makes it an excellent model to study cell specification and the establishment of morphogenetic patterns. Flowers are the products of floral meristems, which are determinate structures that generate four different types of floral organs before terminating. The precise organization of the flower in whorls, each defined by the identity and number of organs it contains, is controlled by a multi-layered network involving numerous transcriptional regulators. In particular, the AGAMOUS (AG) MADS domain-containing transcription factor plays a major role in controlling floral determinacy in Arabidopsis thaliana in addition to specifying reproductive organ identity. This study aims to characterize the genetic interactions between the ULTRAPETALA1 (ULT1) and LEAFY (LFY) transcriptional regulators during flower morphogenesis, with a focus on AG regulation. METHODS Genetic and molecular approaches were used to address the question of redundancy and reciprocal interdependency for the establishment of flower meristem initiation, identity and termination. In particular, the effects of loss of both ULT1 and LFY function were determined by analysing flower developmental phenotypes of double-mutant plants. The dependency of each factor on the other for activating developmental genes was also investigated in gain-of-function experiments. KEY RESULTS The ULT1 and LFY pathways, while both activating AG expression in the centre of the flower meristem, functioned independently in floral meristem determinacy. Ectopic transcriptional activation by ULT1 of AG and AP3, another gene encoding a MADS domain-containing flower architect, did not depend on LFY function. Similarly, LFY did not require ULT1 function to ectopically determine floral fate. CONCLUSIONS The results indicate that the ULT1 and LFY pathways act separately in regulating identity and determinacy at the floral meristem. In particular, they independently induce AG expression in the centre of the flower to terminate meristem activity. A model is proposed whereby these independent contributions bring about a switch at the AG locus from an inactive to an active transcriptional state at the correct time and place during flower development.
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Affiliation(s)
- Julia Engelhorn
- Université Grenoble Alpes, UMR5168, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, F-38054 Grenoble, France
| | - Fanny Moreau
- Université Grenoble Alpes, UMR5168, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, F-38054 Grenoble, France
| | - Jennifer C Fletcher
- Plant Gene Expression Center, USDA-ARS/University of California, Berkeley, 800 Buchanan Street, Albany, CA 94710, USA
| | - Cristel C Carles
- Université Grenoble Alpes, UMR5168, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, F-38054 Grenoble, France
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Pires HR, Monfared MM, Shemyakina EA, Fletcher JC. ULTRAPETALA trxG genes interact with KANADI transcription factor genes to regulate Arabidopsis gynoecium patterning. THE PLANT CELL 2014; 26:4345-61. [PMID: 25381352 PMCID: PMC4277222 DOI: 10.1105/tpc.114.131250] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 09/30/2014] [Accepted: 10/16/2014] [Indexed: 05/13/2023]
Abstract
Organ formation relies upon precise patterns of gene expression that are under tight spatial and temporal regulation. Transcription patterns are specified by several cellular processes during development, including chromatin remodeling, but little is known about how chromatin-remodeling factors contribute to plant organogenesis. We demonstrate that the trithorax group (trxG) gene ULTRAPETALA1 (ULT1) and the GARP transcription factor gene KANADI1 (KAN1) organize the Arabidopsis thaliana gynoecium along two distinct polarity axes. We show that ULT1 activity is required for the kan1 adaxialized polarity defect, indicating that ULT1 and KAN1 act oppositely to regulate the adaxial-abaxial axis. Conversely, ULT1 and KAN1 together establish apical-basal polarity by promoting basal cell fate in the gynoecium, restricting the expression domain of the basic helix-loop-helix transcription factor gene SPATULA. Finally, we show that ult alleles display dose-dependent genetic interactions with kan alleles and that ULT and KAN proteins can associate physically. Our findings identify a dual role for plant trxG factors in organ patterning, with ULT1 and KAN1 acting antagonistically to pattern the adaxial-abaxial polarity axis but jointly to pattern the apical-basal axis. Our data indicate that the ULT proteins function to link chromatin-remodeling factors with DNA binding transcription factors to regulate target gene expression.
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Affiliation(s)
- Helena R Pires
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service/UC Berkeley, Albany, California 94710Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Mona M Monfared
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service/UC Berkeley, Albany, California 94710Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Elena A Shemyakina
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service/UC Berkeley, Albany, California 94710Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Jennifer C Fletcher
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service/UC Berkeley, Albany, California 94710Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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Fromm M, Avramova Z. ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes? CURRENT OPINION IN PLANT BIOLOGY 2014; 21:75-82. [PMID: 25047977 DOI: 10.1016/j.pbi.2014.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/26/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
Despite the proven correlation between gene transcriptional activity and the levels of tri-methyl marks on histone 3 lysine4 (H3K4me3) of their nucleosomes, whether H3K4me3 contributes to, or 'registers', activated transcription is still controversial. Other questions of broad relevance are whether histone-modifying proteins are involved in the recruitment of Pol II and the general transcription machinery and whether they have roles other than their enzyme activities. We address these questions as well as the roles of the ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), of the COMPASS-related (AtCOMPASS) protein complex, and of their product, H3K4me3, at ATX1-dependent genes. We suggest that the ambiguity about the role of H3K4me3 as an activating mark is due to the unknown duality of the ATX1/AtCOMPASS to facilitate PIC assembly and to generate H3K4me3, which is essential for activating transcriptional elongation.
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Affiliation(s)
- Michael Fromm
- Department of Agronomy and Plant Science Innovation, UNL, Lincoln, NE 68588-6008, USA
| | - Zoya Avramova
- School of Biological Science, UNL, Lincoln, NE 68588-6008, USA.
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Leblanc-Fournier N, Martin L, Lenne C, Decourteix M. To respond or not to respond, the recurring question in plant mechanosensitivity. FRONTIERS IN PLANT SCIENCE 2014; 5:401. [PMID: 25177327 PMCID: PMC4132296 DOI: 10.3389/fpls.2014.00401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/28/2014] [Indexed: 05/23/2023]
Abstract
In nature, terrestrial plants experience many kinds of external mechanical stimulation and respond by triggering a network of signaling events to acclimate their growth and development. Some environmental cues, especially wind, recur on time scales varying from seconds to days. Plants thus have to adapt their sensitivity to such stimulations to avoid constitutive activation of stress responses. The study of plant mechanosensing has been attracting more interest in the last two decades, but plant responses to repetitive mechanical stimulation have yet to be described in detail. In this mini review, alongside classic experiments we survey recent descriptions of the kinetics of plant responses to recurrent stimulation. The ability of plants to modulate their responses to recurrent stimulation at the molecular, cellular, or organ scale is also relevant to other abiotic stimuli. It is possible that plants reduce their responsiveness to environmental signals as a function of their recurrence, recovering full sensitivity several days later. Finally, putative mechanisms underlying mechanosensing regulation are discussed.
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Affiliation(s)
- Nathalie Leblanc-Fournier
- Clermont Université – Université Blaise Pascal, UMR547 PIAF, Clermont-FerrandFrance
- INRA, UMR547 PIAF, Clermont-FerrandFrance
| | - Ludovic Martin
- Laboratoire de Biologie du Développement des Plantes, UMR 7265, Centre National de la Recherche Scientifique/Commissariat à l’Energie Atomique/Aix-Marseille Université, Saint-Paul-lez-DuranceFrance
| | - Catherine Lenne
- Clermont Université – Université Blaise Pascal, UMR547 PIAF, Clermont-FerrandFrance
- INRA, UMR547 PIAF, Clermont-FerrandFrance
| | - Mélanie Decourteix
- Clermont Université – Université Blaise Pascal, UMR547 PIAF, Clermont-FerrandFrance
- INRA, UMR547 PIAF, Clermont-FerrandFrance
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50
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Engelhorn J, Blanvillain R, Carles CC. Gene activation and cell fate control in plants: a chromatin perspective. Cell Mol Life Sci 2014; 71:3119-37. [PMID: 24714879 PMCID: PMC11113918 DOI: 10.1007/s00018-014-1609-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/02/2023]
Abstract
In plants, environment-adaptable organogenesis extends throughout the lifespan, and iterative development requires repetitive rounds of activation and repression of several sets of genes. Eukaryotic genome compaction into chromatin forms a physical barrier for transcription; therefore, induction of gene expression requires alteration in chromatin structure. One of the present great challenges in molecular and developmental biology is to understand how chromatin is brought from a repressive to permissive state on specific loci and in a very specific cluster of cells, as well as how this state is further maintained and propagated through time and cell division in a cell lineage. In this review, we report recent discoveries implementing our knowledge on chromatin dynamics that modulate developmental gene expression. We also discuss how new data sets highlight plant specificities, likely reflecting requirement for a highly dynamic chromatin.
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Affiliation(s)
- Julia Engelhorn
- Université Grenoble Alpes, UMR5168, 38041, Grenoble, France,
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