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Wang Y, Sun X, Peng J, Li F, Ali F, Wang Z. Regulation of seed germination: ROS, epigenetic, and hormonal aspects. J Adv Res 2024:S2090-1232(24)00225-X. [PMID: 38838783 DOI: 10.1016/j.jare.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus. AIM of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement. KEY SCIENTIFIC CONCEPTS OF REVIEW We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.
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Affiliation(s)
- Yakong Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiangyang Sun
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jun Peng
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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2
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Zhu T, Wei C, Yu Y, Zhang Z, Zhu J, Liang Z, Song X, Fu W, Cui Y, Wang ZY, Li C. The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis. Dev Cell 2024; 59:924-939.e6. [PMID: 38359831 PMCID: PMC11003849 DOI: 10.1016/j.devcel.2024.01.021] [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: 08/02/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
Brassinosteroid (BR) signaling leads to the nuclear accumulation of the BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor, which plays dual roles in activating or repressing the expression of thousands of genes. BZR1 represses gene expression by recruiting histone deacetylases, but how it activates transcription of BR-induced genes remains unclear. Here, we show that BR reshapes the genome-wide chromatin accessibility landscape, increasing the accessibility of BR-induced genes and reducing the accessibility of BR-repressed genes in Arabidopsis. BZR1 physically interacts with the BRAHMA-associated SWI/SNF (BAS)-chromatin-remodeling complex on the genome and selectively recruits the BAS complex to BR-activated genes. Depletion of BAS abrogates the capacities of BZR1 to increase chromatin accessibility, activate gene expression, and promote cell elongation without affecting BZR1's ability to reduce chromatin accessibility and expression of BR-repressed genes. Together, these data identify that BZR1 recruits the BAS complex to open chromatin and to mediate BR-induced transcriptional activation of growth-promoting genes.
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Affiliation(s)
- Tao Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chuangqi Wei
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhenzhen Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiameng Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-food Canada, London, ON N5V 4T3, Canada
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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3
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Wang Y, Zeng Q, Tian Y, Deng Q, Xiao R, Luo X, Zeng T, Zhang F, Zhang L, Jiang B, Liu Q. The histone deacetylase SRT2 enhances the tolerance of chrysanthemum to low temperatures through the ROS scavenging system. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108405. [PMID: 38354529 DOI: 10.1016/j.plaphy.2024.108405] [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: 10/23/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024]
Abstract
Low temperatures can severely affect plant growth and reduce their ornamental value. A family of plant histone deacetylases allows plants to cope with both biotic and abiotic stresses. In this study, we screened and cloned the cDNA of DgSRT2 obtained from transcriptome sequencing of chrysanthemum leaves under low-temperature stress. Sequence analysis showed that DgSRT2 belongs to the sirtuin family of histone deacetylases. We obtained the stable transgenic chrysanthemum lines OE-2 and OE-12. DgSRT2 showed tissue specificity in wild-type chrysanthemum and was most highly expressed in leaves. Under low-temperature stress, the OE lines showed higher survival rates, proline content, solute content, and antioxidant enzyme activities, and lower relative electrolyte leakage, malondialdehyde, hydrogen peroxide, and superoxide ion accumulation than the wild-type lines. This work suggests that DgSRT2 can serve as an essential gene for enhancing cold resistance in plants. In addition, a series of cold-responsive genes in the OE line were compared with WT. The results showed that DgSRT2 exerted a positive regulatory effect by up-regulating the transcript levels of cold-responsive genes. The above genes help to increase antioxidant activity, maintain membrane stability and improve osmoregulation, thereby enhancing survival under cold stress. It can be concluded from the above work that DgSRT2 enhances chrysanthemum tolerance to low temperatures by scavenging the ROS system.
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Affiliation(s)
- Yongyan Wang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Qinhan Zeng
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Yuchen Tian
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Qingwu Deng
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Runsi Xiao
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Xuanling Luo
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Tao Zeng
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Fan Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Beibei Jiang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
| | - Qinglin Liu
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China.
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4
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Lin X, Yuan T, Guo H, Guo Y, Yamaguchi N, Wang S, Zhang D, Qi D, Li J, Chen Q, Liu X, Zhao L, Xiao J, Wagner D, Cui S, Zhao H. The regulation of chromatin configuration at AGAMOUS locus by LFR-SYD-containing complex is critical for reproductive organ development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:478-496. [PMID: 37478313 DOI: 10.1111/tpj.16385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/28/2023] [Accepted: 06/27/2023] [Indexed: 07/23/2023]
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are evolutionarily conserved, multi-subunit machinery that play vital roles in the regulation of gene expression by controlling nucleosome positioning and occupancy. However, little is known about the subunit composition of SPLAYED (SYD)-containing SWI/SNF complexes in plants. Here, we show that the Arabidopsis thaliana Leaf and Flower Related (LFR) is a subunit of SYD-containing SWI/SNF complexes. LFR interacts directly with multiple SWI/SNF subunits, including the catalytic ATPase subunit SYD, in vitro and in vivo. Phenotypic analyses of lfr-2 mutant flowers revealed that LFR is important for proper filament and pistil development, resembling the function of SYD. Transcriptome profiling revealed that LFR and SYD shared a subset of co-regulated genes. We further demonstrate that the LFR and SYD interdependently activate the transcription of AGAMOUS (AG), a C-class floral organ identity gene, by regulating the occupation of nucleosome, chromatin loop, histone modification, and Pol II enrichment on the AG locus. Furthermore, the chromosome conformation capture (3C) assay revealed that the gene loop at AG locus is negatively correlated with the AG expression level, and LFR-SYD was functional to demolish the AG chromatin loop to promote its transcription. Collectively, these results provide insight into the molecular mechanism of the Arabidopsis SYD-SWI/SNF complex in the control of higher chromatin conformation of the floral identity gene essential to plant reproductive organ development.
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Affiliation(s)
- Xiaowei Lin
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
- School of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Tingting Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Hong Guo
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yi Guo
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Nobutoshi Yamaguchi
- Biological Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Shuge Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Dongxia Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Dongmei Qi
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Jiayu Li
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Qiang Chen
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xinye Liu
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Long Zhao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jun Xiao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, 19104-6084, Pennsylvania, USA
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
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5
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Guo J, Cai G, Li YQ, Zhang YX, Su YN, Yuan DY, Zhang ZC, Liu ZZ, Cai XW, Guo J, Li L, Chen S, He XJ. Comprehensive characterization of three classes of Arabidopsis SWI/SNF chromatin remodelling complexes. NATURE PLANTS 2022; 8:1423-1439. [PMID: 36471048 DOI: 10.1038/s41477-022-01282-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
Although SWI/SNF chromatin remodelling complexes are known to regulate diverse biological functions in plants, the classification, compositions and functional mechanisms of the complexes remain to be determined. Here we comprehensively characterized SWI/SNF complexes by affinity purification and mass spectrometry in Arabidopsis thaliana, and found three classes of SWI/SNF complexes, which we termed BAS, SAS and MAS (BRM-, SYD- and MINU1/2-associated SWI/SNF complexes). By investigating multiple developmental phenotypes of SWI/SNF mutants, we found that three classes of SWI/SNF complexes have both overlapping and specific functions in regulating development. To investigate how the three classes of SWI/SNF complexes differentially regulate development, we mapped different SWI/SNF components on chromatin at the whole-genome level and determined their effects on chromatin accessibility. While all three classes of SWI/SNF complexes regulate chromatin accessibility at proximal promoter regions, SAS is a major SWI/SNF complex that is responsible for mediating chromatin accessibility at distal promoter regions and intergenic regions. Histone modifications are related to both the association of SWI/SNF complexes with chromatin and the SWI/SNF-dependent chromatin accessibility. Three classes of SWI/SNF-dependent accessibility may enable different sets of transcription factors to access chromatin. These findings lay a foundation for further investigation of the function of three classes of SWI/SNF complexes in plants.
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Affiliation(s)
- Jing Guo
- College of Life Sciences, Beijing Normal University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Guang Cai
- National Institute of Biological Sciences, Beijing, China
| | - Yong-Qiang Li
- National Institute of Biological Sciences, Beijing, China
| | - Yi-Xuan Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, China
| | - Dan-Yang Yuan
- National Institute of Biological Sciences, Beijing, China
| | | | - Zhen-Zhen Liu
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, China
| | - Jing Guo
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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6
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Kang H, Fan T, Wu J, Zhu Y, Shen WH. Histone modification and chromatin remodeling in plant response to pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:986940. [PMID: 36262654 PMCID: PMC9574397 DOI: 10.3389/fpls.2022.986940] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
As sessile organisms, plants are constantly exposed to changing environments frequently under diverse stresses. Invasion by pathogens, including virus, bacterial and fungal infections, can severely impede plant growth and development, causing important yield loss and thus challenging food/feed security worldwide. During evolution, plants have adapted complex systems, including coordinated global gene expression networks, to defend against pathogen attacks. In recent years, growing evidences indicate that pathogen infections can trigger local and global epigenetic changes that reprogram the transcription of plant defense genes, which in turn helps plants to fight against pathogens. Here, we summarize up plant defense pathways and epigenetic mechanisms and we review in depth current knowledge's about histone modifications and chromatin-remodeling factors found in the epigenetic regulation of plant response to biotic stresses. It is anticipated that epigenetic mechanisms may be explorable in the design of tools to generate stress-resistant plant varieties.
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Affiliation(s)
- Huijia Kang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| | - Tianyi Fan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
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7
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Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
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Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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8
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Wu X, Xu J, Meng X, Fang X, Xia M, Zhang J, Cao S, Fan T. Linker histone variant HIS1-3 and WRKY1 oppositely regulate salt stress tolerance in Arabidopsis. PLANT PHYSIOLOGY 2022; 189:1833-1847. [PMID: 35474141 PMCID: PMC9237719 DOI: 10.1093/plphys/kiac174] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/03/2021] [Indexed: 06/12/2023]
Abstract
The salt overly sensitive (SOS) pathway plays an important role in plant salt stress; however, the transcriptional regulation of the genes in this pathway is unclear. In this study, we found that Linker histone variant HIS1-3 and WRKY1 oppositely regulate the salt stress response in Arabidopsis (Arabidopsis thaliana) through the transcriptional regulation of SOS genes. The expression of HIS1-3 was inhibited by salt stress, and the disruption of HIS1-3 resulted in enhanced salt tolerance. Conversely, the expression of WRKY1 was induced by salt stress, and the loss of WRKY1 function led to increased salt sensitivity. The expression of SOS1, SOS2, and SOS3 was repressed and induced by HIS1-3 and WRKY1, respectively, and HIS1-3 regulated the expression of SOS1 and SOS3 by occupying the WRKY1 binding sites on their promoters. Moreover, WRKY1 and HIS1-3 acted upstream of the SOS pathway. Together, our results indicate that HIS1-3 and WRKY1 oppositely modulate salt tolerance in Arabidopsis through transcriptional regulation of SOS genes.
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Affiliation(s)
| | | | | | - Xue Fang
- School of Horticulture, Anhui Agricultural University, Hefei 230009, China
| | - Minghui Xia
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jing Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shuqing Cao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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9
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Hernández-García J, Diego-Martin B, Kuo PH, Jami-Alahmadi Y, Vashisht AA, Wohlschlegel J, Jacobsen SE, Blázquez MA, Gallego-Bartolomé J. Comprehensive identification of SWI/SNF complex subunits underpins deep eukaryotic ancestry and reveals new plant components. Commun Biol 2022; 5:549. [PMID: 35668117 PMCID: PMC9170682 DOI: 10.1038/s42003-022-03490-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/16/2022] [Indexed: 01/19/2023] Open
Abstract
Over millions of years, eukaryotes evolved from unicellular to multicellular organisms with increasingly complex genomes and sophisticated gene expression networks. Consequently, chromatin regulators evolved to support this increased complexity. The ATP-dependent chromatin remodelers of the SWI/SNF family are multiprotein complexes that modulate nucleosome positioning and appear under different configurations, which perform distinct functions. While the composition, architecture, and activity of these subclasses are well understood in a limited number of fungal and animal model organisms, the lack of comprehensive information in other eukaryotic organisms precludes the identification of a reliable evolutionary model of SWI/SNF complexes. Here, we performed a systematic analysis using 36 species from animal, fungal, and plant lineages to assess the conservation of known SWI/SNF subunits across eukaryotes. We identified evolutionary relationships that allowed us to propose the composition of a hypothetical ancestral SWI/SNF complex in the last eukaryotic common ancestor. This last common ancestor appears to have undergone several rounds of lineage-specific subunit gains and losses, shaping the current conformation of the known subclasses in animals and fungi. In addition, our results unravel a plant SWI/SNF complex, reminiscent of the animal BAF subclass, which incorporates a set of plant-specific subunits of still unknown function.
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Affiliation(s)
- Jorge Hernández-García
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
- Laboratory of Biochemistry, Wageningen University & Research, 6703 WE, Stippeneng 4, Wageningen, The Netherlands
| | - Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Peggy Hsuanyu Kuo
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, 90095, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, 90095, CA, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, 90095, CA, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, 90095, CA, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, 90095, CA, USA
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, 90095, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, 90095, CA, USA
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain.
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10
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Yang J, Xu Y, Wang J, Gao S, Huang Y, Hung FY, Li T, Li Q, Yue L, Wu K, Yang S. The chromatin remodelling ATPase BRAHMA interacts with GATA-family transcription factor GNC to regulate flowering time in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:835-847. [PMID: 34545936 DOI: 10.1093/jxb/erab430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/20/2021] [Indexed: 05/13/2023]
Abstract
BRAHMA (BRM) is the ATPase of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodelling complex, which is indispensable for transcriptional inhibition and activation, associated with vegetative and reproductive development in Arabidopsis thaliana. Here, we show that BRM directly binds to the chromatin of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), which integrates multiple flowering signals to regulate floral transition, leading to flowering. In addition, genetic and molecular analysis showed that BRM interacts with GNC (GATA, NITRATE-INDUCIBLE, CARBON METABOLISM INVOLVED), a GATA transcription factor that represses flowering by directly repressing SOC1 expression. Furthermore, BRM is recruited by GNC to directly bind to the chromatin of SOC1. The transcript level of SOC1 is elevated in brm-3, gnc, and brm-3/gnc mutants, which is associated with increased histone H3 lysine 4 tri-methylation (H3K4Me3) but decreased DNA methylation. Taken together, our results indicate that BRM associates with GNC to regulate SOC1 expression and flowering time.
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Affiliation(s)
- Jie Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhao Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Sujuan Gao
- College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yisui Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Tao Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qing Li
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agrobiological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Lin Yue
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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11
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Banerjee S, Roy S. An insight into understanding the coupling between homologous recombination mediated DNA repair and chromatin remodeling mechanisms in plant genome: an update. Cell Cycle 2021; 20:1760-1784. [PMID: 34437813 DOI: 10.1080/15384101.2021.1966584] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Plants, with their obligatory immobility, are vastly exposed to a wide range of environmental agents and also various endogenous processes, which frequently cause damage to DNA and impose genotoxic stress. These factors subsequently increase genome instability, thus affecting plant growth and productivity. Therefore, to survive under frequent and extreme environmental stress conditions, plants have developed highly efficient and powerful defense mechanisms to repair the damages in the genome for maintaining genome stability. Such multi-dimensional signaling response, activated in presence of damage in the DNA, is collectively known as DNA Damage Response (DDR). DDR plays a crucial role in the remarkably efficient detection, signaling, and repair of damages in the genome for maintaining plant genome stability and normal growth responses. Like other highly advanced eukaryotic systems, chromatin dynamics play a key role in regulating cell cycle progression in plants through remarkable orchestration of environmental and developmental signals. The regulation of chromatin architecture and nucleosomal organization in DDR is mainly modulated by the ATP dependent chromatin remodelers (ACRs), chromatin modifiers, and histone chaperones. ACRs are mainly responsible for transcriptional regulation of several homologous recombination (HR) repair genes in plants under genotoxic stress. The HR-based repair of DNA damage has been considered as the most error-free mechanism of repair and represents one of the essential sources of genetic diversity and new allelic combinations in plants. The initiation of DDR signaling and DNA damage repair pathway requires recruitment of epigenetic modifiers for remodeling of the damaged chromatin while accumulating evidence has shown that chromatin remodeling and DDR share part of the similar signaling pathway through the altered epigenetic status of the associated chromatin region. In this review, we have integrated information to provide an overview on the association between chromatin remodeling mediated regulation of chromatin structure stability and DDR signaling in plants, with emphasis on the scope of the utilization of the available knowledge for the improvement of plant health and productivity.Abbreviation: ADH: Alcohol Dehydrogenase; AGO2: Argonaute 2; ARP: Actin-Related Protein; ASF:1- Anti-Silencing Function-1; ATM: Ataxia Telangiectasia Mutated; ATR: ATM and Rad3- Related; AtSWI3c: Arabidopsis thaliana Switch 3c; ATXR5: Arabidopsis Trithorax-Related5; ATXR6: Arabidopsis Trithorax-Related6; BER: Base Excision Repair; BRCA1: Breast Cancer Associated 1; BRM: BRAHMA; BRU1: BRUSHY1; CAF:1- Chromatin Assembly Factor-1; CHD: Chromodomain Helicase DNA; CHR5: Chromatin Remodeling Protein 5; CHR11/17: Chromatin Remodeling Protein 11/17; CIPK11- CBL- Interacting Protein Kinase 11; CLF: Curly Leaf; CMT3: Chromomethylase 3; COR15A: Cold Regulated 15A; COR47: Cold Regulated 47; CRISPR: Clustered Regulatory Interspaced Short Palindromic Repeats; DDM1: Decreased DNA Methylation1; DRR: DNA Repair and Recombination; DSBs: Double-Strand Breaks; DDR: DNA Damage Response; EXO1: Exonuclease 1; FAS1/2: Fasciata1/2; FACT: Facilitates Chromatin Transcription; FT: Flowering Locus T; GMI1: Gamma-Irradiation And Mitomycin C Induced 1; HAC1: Histone Acetyltransferase of the CBP Family 1; HAM1: Histone Acetyltransferase of the MYST Family 1; HAM2: Histone Acetyltransferase of the MYST Family 2; HAF1: Histone Acetyltransferase of the TAF Family 1; HAT: Histone Acetyl Transferase; HDA1: Histone Deacetylase 1; HDA6: Histone Deacetylase 6; HIRA: Histone Regulatory Homolog A; HR- Homologous recombination; HAS: Helicase SANT Associated; HSS: HAND-SLANT-SLIDE; ICE1: Inducer of CBF Expression 1; INO80: Inositol Requiring Mutant 80; ISW1: Imitation Switch 1; KIN1/2: Kinase 1 /2; MET1: Methyltransferase 1; MET2: Methyltransferase 2; MINU: MINUSCULE; MMS: Methyl Methane Sulfonate; MMS21: Methyl Methane Sulfonate Sensitivity 21; MRN: MRE11, RAD50 and NBS1; MSI1: Multicopy Suppressor Of Ira1; NAP1: Nucleosome Assembly Protein 1; NRP1/NRP2: NAP1-Related Protein; NER: Nucleotide Excision Repair; NHEJ: Non-Homologous End Joining; PARP1: Poly-ADP Ribose Polymerase; PIE1: Photoperiod Independent Early Flowering 1; PIKK: Phosphoinositide 3-Kinase-Like Kinase; PKL: PICKLE; PKR1/2: PICKLE Related 1/2; RAD: Radiation Sensitive Mutant; RD22: Responsive To Desiccation 22; RD29A: Responsive To Desiccation 29A; ROS: Reactive Oxygen Species; ROS1: Repressor of Silencing 1; RPA1E: Replication Protein A 1E; SANT: Swi3, Ada2, N-Cor and TFIIIB; SEP3: SEPALLATA3; SCC3: Sister Chromatid Cohesion Protein 3; SMC1: Structural Maintenance of Chromosomes Protein 1; SMC3: Structural Maintenance of Chromosomes Protein 3; SOG1: Suppressor of Gamma Response 1; SWC6: SWR1 Complex Subunit 6; SWR1: SWI2/SNF2-Related 1; SYD: SPLAYED; SMC5: Structural Maintenance of Chromosome 5; SWI/SNF: Switch/Sucrose Non-Fermentable; TALENs: Transcription Activators Like Effector Nucleases; TRRAP: Transformation/Transactivation Domain-Associated Protein; ZFNs: Zinc Finger Nucleases.
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Affiliation(s)
- Samrat Banerjee
- Department of Botany, UGC Centre for Advanced Studies, the University of Burdwan, Golapbag Campus, Burdwan, West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Centre for Advanced Studies, the University of Burdwan, Golapbag Campus, Burdwan, West Bengal, India
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12
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Jarończyk K, Sosnowska K, Zaborowski A, Pupel P, Bucholc M, Małecka E, Siwirykow N, Stachula P, Iwanicka-Nowicka R, Koblowska M, Jerzmanowski A, Archacki R. Bromodomain-containing subunits BRD1, BRD2, and BRD13 are required for proper functioning of SWI/SNF complexes in Arabidopsis. PLANT COMMUNICATIONS 2021; 2:100174. [PMID: 34327319 PMCID: PMC8299063 DOI: 10.1016/j.xplc.2021.100174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/12/2021] [Accepted: 03/02/2021] [Indexed: 05/26/2023]
Abstract
SWI/SNF chromatin remodelers are evolutionarily conserved multiprotein complexes that use the energy of ATP hydrolysis to change chromatin structure. A characteristic feature of SWI/SNF remodelers is the occurrence in both the catalytic ATPase subunit and some auxiliary subunits, of bromodomains, the protein motifs capable of binding acetylated histones. Here, we report that the Arabidopsis bromodomain-containing proteins BRD1, BRD2, and BRD13 are likely true SWI/SNF subunits that interact with the core SWI/SNF components SWI3C and SWP73B. Loss of function of each single BRD protein caused early flowering but had a negligible effect on other developmental pathways. By contrast, a brd triple mutation (brdx3) led to more pronounced developmental abnormalities, indicating functional redundancy among the BRD proteins. The brdx3 phenotypes, including hypersensitivity to abscisic acid and the gibberellin biosynthesis inhibitor paclobutrazol, resembled those of swi/snf mutants. Furthermore, the BRM protein level and occupancy at the direct target loci SCL3, ABI5, and SVP were reduced in the brdx3 mutant background. Finally, a brdx3 brm-3 quadruple mutant, in which SWI/SNF complexes were devoid of all constituent bromodomains, phenocopied a loss-of-function mutation in BRM. Taken together, our results demonstrate the relevance of BRDs as SWI/SNF subunits and suggest their cooperation with the bromodomain of BRM ATPase.
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Affiliation(s)
- Kamila Jarończyk
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | | | - Adam Zaborowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Piotr Pupel
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
| | - Maria Bucholc
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Ewelina Małecka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Nina Siwirykow
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Paulina Stachula
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Rafał Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
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13
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Blanco-Pastor JL, Liberal IM, Sakiroglu M, Wei Y, Brummer EC, Andrew RL, Pfeil BE. Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes. Mol Ecol 2021; 30:4448-4465. [PMID: 34217151 DOI: 10.1111/mec.16061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analysed polymorphic loci from the perennial crop Medicago sativa (alfalfa or lucerne) and the annual legume model species M. truncatula to search for a common set of candidate genes that might contribute to adaptation to abiotic stress in both annual and perennial Medicago species. We identified a set of candidate genes of adaptation associated with environmental gradients along the distribution of the two Medicago species. Candidate genes for each species were detected in homologous genomic linkage blocks using genome-environment (GEA) and genome-phenotype association analyses. Hundreds of GEA candidate genes were species-specific, of these, 13.4% (M. sativa) and 24% (M. truncatula) were also significantly associated with phenotypic traits. A set of 168 GEA candidates were shared by both species, which was 25.4% more than expected by chance. When combined, they explained a high proportion of variance for certain phenotypic traits associated with adaptation. Genes with highly conserved functions dominated among the shared candidates and were enriched in gene ontology terms that have shown to play a central role in drought avoidance and tolerance mechanisms by means of cellular shape modifications and other functions associated with cell homeostasis. Our results point to the existence of a molecular basis of adaptation to abiotic stress in Medicago determined by highly conserved genes and gene functions. We discuss these results in light of the recently proposed omnigenic model of complex traits.
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Affiliation(s)
- José Luis Blanco-Pastor
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,INRAE, Centre Nouvelle-Aquitaine-Poitiers, UR4 (URP3F), Lusignan, France
| | - Isabel M Liberal
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Real Jardín Botánico de Madrid (RJB-CSIC), Madrid, Spain
| | - Muhammet Sakiroglu
- Department of Bioengineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
| | - Yanling Wei
- Plant Breeding Center, Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - E Charles Brummer
- Plant Breeding Center, Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Bernard E Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
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14
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Yu Y, Fu W, Xu J, Lei Y, Song X, Liang Z, Zhu T, Liang Y, Hao Y, Yuan L, Li C. Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis. MOLECULAR PLANT 2021; 14:888-904. [PMID: 33771698 DOI: 10.1016/j.molp.2021.03.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 05/26/2023]
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machines that play vital roles in the regulation of chromatin structure and gene expression. However, the mechanisms by which SWI/SNF complexes recognize their target loci in plants are not fully understood. Here, we show that the Arabidopsis thaliana bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and critical for SWI/SNF genomic targeting. These three BRDs interact directly with multiple SWI/SNF subunits, including the BRAHMA (BRM) catalytic subunit. Phenotypic and transcriptomic analyses of the brd1 brd2 brd13 triple mutant revealed that these BRDs act largely redundantly to control gene expression and developmental processes that are also regulated by BRM. Genome-wide occupancy profiling demonstrated that these three BRDs extensively colocalize with BRM on chromatin. Simultaneous loss of function of three BRD genes results in reduced BRM protein levels and decreased occupancy of BRM on chromatin across the genome. Furthermore, we demonstrated that the bromodomains of BRDs are essential for genomic targeting of the BRD subunits of SWI/SNF complexes to their target sites. Collectively, these results demonstrate that BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and reveal their biological roles in facilitating genomic targeting of BRM-containing SWI/SNF complexes in plants.
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Affiliation(s)
- Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jianqu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yawen Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuhui Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuanhao Hao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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15
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Song ZT, Liu JX, Han JJ. Chromatin remodeling factors regulate environmental stress responses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:438-450. [PMID: 33421288 DOI: 10.1111/jipb.13064] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/23/2020] [Indexed: 05/14/2023]
Abstract
Environmental stress from climate change and agricultural activity threatens global plant biodiversity as well as crop yield and quality. As sessile organisms, plants must maintain the integrity of their genomes and adjust gene expression to adapt to various environmental changes. In eukaryotes, nucleosomes are the basic unit of chromatin around which genomic DNA is packaged by condensation. To enable dynamic access to packaged DNA, eukaryotes have evolved Snf2 (sucrose nonfermenting 2) family proteins as chromatin remodeling factors (CHRs) that modulate the position of nucleosomes on chromatin. During plant stress responses, CHRs are recruited to specific genomic loci, where they regulate the distribution or composition of nucleosomes, which in turn alters the accessibility of these loci to general transcription or DNA damage repair machinery. Moreover, CHRs interplay with other epigenetic mechanisms, including DNA methylation, histone modifications, and deposition of histone variants. CHRs are also involved in RNA processing at the post-transcriptional level. In this review, we discuss major advances in our understanding of the mechanisms by which CHRs function during plants' response to environmental stress.
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Affiliation(s)
- Ze-Ting Song
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- 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
| | - Jia-Jia Han
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500, China
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16
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Hnatuszko-Konka K, Gerszberg A, Weremczuk-Jeżyna I, Grzegorczyk-Karolak I. Cytokinin Signaling and De Novo Shoot Organogenesis. Genes (Basel) 2021; 12:265. [PMID: 33673064 PMCID: PMC7917986 DOI: 10.3390/genes12020265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 11/16/2022] Open
Abstract
The ability to restore or replace injured tissues can be undoubtedly named among the most spectacular achievements of plant organisms. One of such regeneration pathways is organogenesis, the formation of individual organs from nonmeristematic tissue sections. The process can be triggered in vitro by incubation on medium supplemented with phytohormones. Cytokinins are a class of phytohormones demonstrating pleiotropic effects and a powerful network of molecular interactions. The present study reviews existing knowledge on the possible sequence of molecular and genetic events behind de novo shoot organogenesis initiated by cytokinins. Overall, the review aims to collect reactions encompassed by cytokinin primary responses, starting from phytohormone perception by the dedicated receptors, to transcriptional reprogramming of cell fate by the last module of multistep-phosphorelays. It also includes a brief reminder of other control mechanisms, such as epigenetic reprogramming.
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Affiliation(s)
- Katarzyna Hnatuszko-Konka
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
| | - Aneta Gerszberg
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
| | - Izabela Weremczuk-Jeżyna
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (I.W.-J.); (I.G.-K.)
| | - Izabela Grzegorczyk-Karolak
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (I.W.-J.); (I.G.-K.)
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17
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Huang CY, Rangel DS, Qin X, Bui C, Li R, Jia Z, Cui X, Jin H. The chromatin-remodeling protein BAF60/SWP73A regulates the plant immune receptor NLRs. Cell Host Microbe 2021; 29:425-434.e4. [PMID: 33548199 DOI: 10.1016/j.chom.2021.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/02/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
In both plant and animal innate immune responses, surveillance of pathogen infection is mediated by membrane-associated receptors and intracellular nucleotide-binding domain and leucine-rich-repeat receptors (NLRs). Homeostasis of NLRs is under tight multilayered regulation to avoid over-accumulation or over-activation, which often leads to autoimmune responses that have detrimental effects on growth and development. How NLRs are regulated epigenetically at the chromatin level remains unclear. Here, we report that SWP73A, an ortholog of the mammalian switch/sucrose nonfermentable (SWI/SNF) chromatin-remodeling protein BAF60, suppresses the expression of NLRs either directly by binding to the NLR promoters or indirectly by affecting the alternative splicing of some NLRs through the suppression of cell division cycle 5 (CDC5), a key regulator of RNA splicing. Upon infection, bacteria-induced small RNAs silence SWP73A to activate a group of NLRs and trigger robust immune responses. SWP73A may function as a H3K9me2 reader to enhance transcription suppression.
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Affiliation(s)
- Chien-Yu Huang
- Department of Microbiology & Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521-0122, USA
| | - Diana Sánchez Rangel
- Department of Microbiology & Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521-0122, USA; Cátedra CONACyT en la red de Estudios Moleculares Avanzados del Instituto de Ecología A.C. (INECOL), Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91070, México
| | - Xiaobo Qin
- Department of Microbiology & Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521-0122, USA
| | - Christine Bui
- Department of Microbiology & Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521-0122, USA
| | - Ruidong Li
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Xinping Cui
- Department of Statistics, University of California, Riverside, CA 92521, USA
| | - Hailing Jin
- Department of Microbiology & Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521-0122, USA.
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18
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Bhadouriya SL, Mehrotra S, Basantani MK, Loake GJ, Mehrotra R. Role of Chromatin Architecture in Plant Stress Responses: An Update. FRONTIERS IN PLANT SCIENCE 2021; 11:603380. [PMID: 33510748 PMCID: PMC7835326 DOI: 10.3389/fpls.2020.603380] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/07/2020] [Indexed: 05/08/2023]
Abstract
Sessile plants possess an assembly of signaling pathways that perceive and transmit environmental signals, ultimately resulting in transcriptional reprogramming. Histone is a key feature of chromatin structure. Numerous histone-modifying proteins act under different environmental stress conditions to help modulate gene expression. DNA methylation and histone modification are crucial for genome reprogramming for tissue-specific gene expression and global gene silencing. Different classes of chromatin remodelers including SWI/SNF, ISWI, INO80, and CHD are reported to act upon chromatin in different organisms, under diverse stresses, to convert chromatin from a transcriptionally inactive to a transcriptionally active state. The architecture of chromatin at a given promoter is crucial for determining the transcriptional readout. Further, the connection between somatic memory and chromatin modifications may suggest a mechanistic basis for a stress memory. Studies have suggested that there is a functional connection between changes in nuclear organization and stress conditions. In this review, we discuss the role of chromatin architecture in different stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.
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Affiliation(s)
- Sneha Lata Bhadouriya
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Mahesh K. Basantani
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow, India
| | - Gary J. Loake
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburg, Edinburg, United Kingdom
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
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19
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Nishioka S, Sakamoto T, Matsunaga S. Roles of BRAHMA and Its Interacting Partners in Plant Chromatin Remodeling. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sakiko Nishioka
- Department of Applied Biological Science, Faculty of Science and Technology Tokyo University of Science
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology Tokyo University of Science
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
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20
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Probst AV, Desvoyes B, Gutierrez C. Similar yet critically different: the distribution, dynamics and function of histone variants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5191-5204. [PMID: 32392582 DOI: 10.1093/jxb/eraa230] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2020] [Indexed: 05/23/2023]
Abstract
Organization of the genetic information into chromatin plays an important role in the regulation of all DNA template-based reactions. The incorporation of different variant versions of the core histones H3, H2A, and H2B, or the linker histone H1 results in nucleosomes with unique properties. Histone variants can differ by only a few amino acids or larger protein domains and their incorporation may directly affect nucleosome stability and higher order chromatin organization or indirectly influence chromatin function through histone variant-specific binding partners. Histone variants employ dedicated histone deposition machinery for their timely and locus-specific incorporation into chromatin. Plants have evolved specific histone variants with unique expression patterns and features. In this review, we discuss our current knowledge on histone variants in Arabidopsis, their mode of deposition, variant-specific post-translational modifications, and genome-wide distribution, as well as their role in defining different chromatin states.
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Affiliation(s)
- Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
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21
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Yu Y, Liang Z, Song X, Fu W, Xu J, Lei Y, Yuan L, Ruan J, Chen C, Fu W, Cui Y, Huang S, Li C. BRAHMA-interacting proteins BRIP1 and BRIP2 are core subunits of Arabidopsis SWI/SNF complexes. NATURE PLANTS 2020; 6:996-1007. [PMID: 32747760 DOI: 10.1038/s41477-020-0734-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/29/2020] [Indexed: 05/22/2023]
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodelling complexes are multi-protein machineries that control gene expression by regulating chromatin structure in eukaryotes. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we report that in Arabidopsis thaliana, two homologous glioma tumour suppressor candidate region domain-containing proteins, named BRAHMA-interacting proteins 1 (BRIP1) and BRIP2, are core subunits of plant SWI/SNF complexes. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome remarkably similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and BRIP2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and BRIP2 physically interact with BRM-containing SWI/SNF complexes and extensively co-localize with BRM on chromatin. Simultaneous mutation of BRIP1 and BRIP2 results in decreased BRM occupancy at almost all BRM target loci and substantially reduced abundance of the SWI/SNF assemblies. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants and uncovers the essential role of these subunits in maintaining the abundance of SWI/SNF complexes in plants.
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Affiliation(s)
- Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jianqu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yawen Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chen Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Wenqun Fu
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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22
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Yang J, Chang Y, Qin Y, Chen D, Zhu T, Peng K, Wang H, Tang N, Li X, Wang Y, Liu Y, Li X, Xie W, Xiong L. A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice. THE NEW PHYTOLOGIST 2020; 227:65-83. [PMID: 32129897 DOI: 10.1111/nph.16518] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/18/2020] [Indexed: 05/28/2023]
Abstract
Lamin proteins in animals are implicated in important nuclear functions, including chromatin organization, signalling transduction, gene regulation and cell differentiation. Nuclear Matrix Constituent Proteins (NMCPs) are lamin analogues in plants, but their regulatory functions remain largely unknown. We report that OsNMCP1 is localized at the nuclear periphery in rice (Oryza sativa) and induced by drought stress. OsNMCP1 overexpression resulted in a deeper and thicker root system, and enhanced drought resistance compared to the wild-type control. An assay for transposase accessible chromatin with sequencing (ATAC-seq) analysis revealed that OsNMCP1-overexpression altered chromatin accessibility in hundreds of genes related to drought resistance and root growth, including OsNAC10, OsERF48, OsSGL, SNAC1 and OsbZIP23. OsNMCP1 can interact with SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodelling complex subunit OsSWI3C. The reported drought resistance or root growth-related genes that were positively regulated by OsNMCP1 were negatively regulated by OsSWI3C under drought stress conditions, and OsSWI3C overexpression led to decreased drought resistance. We propose that the interaction between OsNMCP1 and OsSWI3C under drought stress conditions may lead to the release of OsSWI3C from the SWI/SNF gene silencing complex, thus changing chromatin accessibility in the genes related to root growth and drought resistance.
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Affiliation(s)
- Jun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu Chang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yonghua Qin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- South-Central University for Nationalities, Wuhan, 430074, China
| | - Dijun Chen
- Department for Plant Cell and Molecular Biology (AG Kaufmann) Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Tao Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Kaiqing Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Huaijun Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Ning Tang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yusen Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yinmeng Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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23
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Smoczynska A, Pacak AM, Nuc P, Swida-Barteczka A, Kruszka K, Karlowski WM, Jarmolowski A, Szweykowska-Kulinska Z. A Functional Network of Novel Barley MicroRNAs and Their Targets in Response to Drought. Genes (Basel) 2020; 11:genes11050488. [PMID: 32365647 PMCID: PMC7290300 DOI: 10.3390/genes11050488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/27/2022] Open
Abstract
The regulation of mRNA (messenger RNA) levels by microRNA-mediated activity is especially important in plant responses to environmental stresses. In this work, we report six novel barley microRNAs, including two processed from the same precursor that are severely downregulated under drought conditions. For all analyzed microRNAs, we found target genes that were upregulated under drought conditions and that were known to be involved in a plethora of processes from disease resistance to chromatin–protein complex formation and the regulation of transcription in mitochondria. Targets for novel barley microRNAs were confirmed through degradome data analysis and RT-qPCR using primers flanking microRNA-recognition site. Our results show a broad transcriptional response of barley to water deficiency conditions through microRNA-mediated gene regulation and facilitate further research on drought tolerance in crops.
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Affiliation(s)
- Aleksandra Smoczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Andrzej M. Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-712 Poznan, Poland;
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
- Correspondence: ; Tel.: +48-61-829-5950
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24
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Meng X, Yu X, Wu Y, Kim DH, Nan N, Cong W, Wang S, Liu B, Xu ZY. Chromatin Remodeling Protein ZmCHB101 Regulates Nitrate-Responsive Gene Expression in Maize. FRONTIERS IN PLANT SCIENCE 2020; 11:52. [PMID: 32117389 PMCID: PMC7031486 DOI: 10.3389/fpls.2020.00052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/15/2020] [Indexed: 05/24/2023]
Abstract
Nitrate is the main source of nitrogen for plants and an essential component of fertilizers. Rapid transcriptional activation of genes encoding the high-affinity nitrate transport system (HATS) is an important strategy that plants use to cope with nitrogen deficiency. However, the specific transcriptional machineries involved in this process and the detailed transcriptional regulatory mechanism of the core HATS remain poorly understood. ZmCHB101 is the core subunit of the SWI/SNF-type ATP-dependent chromatin remodeling complex in maize. RNA-interference transgenic plants (ZmCHB101-RNAi) display abaxially curling leaves and impaired tassel and cob development. Here, we demonstrate that ZmCHB101 plays a pivotal regulatory role in nitrate-responsive gene expression. ZmCHB101-RNAi lines showed accelerated root growth and increased biomass under low nitrate conditions. An RNA sequencing analysis revealed that ZmCHB101 regulates the expression of genes involved in nitrate transport, including ZmNRT2.1 and ZmNRT2.2. The NIN-like protein (NLP) of maize, ZmNLP3.1, recognized the consensus nitrate-responsive cis-elements (NREs) in the promoter regions of ZmNRT2.1 and ZmNRT2.2, and activated the transcription of these genes in response to nitrate. Intriguingly, well-positioned nucleosomes were detected at NREs in the ZmNRT2.1 and ZmNRT2.2 gene promoters, and nucleosome densities were lower in ZmCHB101-RNAi lines than in wild-type plants, both in the absence and presence of nitrate. The ZmCHB101 protein bound to NREs and was involved in the maintenance of nucleosome occupancies at these sites, which may impact the binding of ZmNLP3.1 to NREs in the absence of nitrate. However, in the presence of nitrate, the binding affinity of ZmCHB101 for NREs decreased dramatically, leading to reduced nucleosome density at NREs and consequently increased ZmNLP3.1 binding. Our results provide novel insights into the role of chromatin remodeling proteins in the regulation of nitrate-responsive gene expression in plants.
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Affiliation(s)
- Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- School of Agronomy, Jilin Agricultural Science and Technology University, Jilin, China
| | - Yifan Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon, South Korea
| | - Nan Nan
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Weixuan Cong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- College of Life Sciences, Linyi University, Linyi, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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25
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Kang H, Wu D, Fan T, Zhu Y. Activities of Chromatin Remodeling Factors and Histone Chaperones and Their Effects in Root Apical Meristem Development. Int J Mol Sci 2020; 21:ijms21030771. [PMID: 31991579 PMCID: PMC7038114 DOI: 10.3390/ijms21030771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic genes are packaged into dynamic but stable chromatin structures to deal with transcriptional reprogramming and inheritance during development. Chromatin remodeling factors and histone chaperones are epigenetic factors that target nucleosomes and/or histones to establish and maintain proper chromatin structures during critical physiological processes such as DNA replication and transcriptional modulation. Root apical meristems are vital for plant root development. Regarding the well-characterized transcription factors involved in stem cell proliferation and differentiation, there is increasing evidence of the functional implications of epigenetic regulation in root apical meristem development. In this review, we focus on the activities of chromatin remodeling factors and histone chaperones in the root apical meristems of the model plant species Arabidopsis and rice.
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26
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Lei B, Berger F. H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity. PLANT COMMUNICATIONS 2020; 1:100015. [PMID: 33404536 PMCID: PMC7747964 DOI: 10.1016/j.xplc.2019.100015] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/13/2019] [Accepted: 12/11/2019] [Indexed: 05/16/2023]
Abstract
The eukaryotic nucleosome prevents access to the genome. Convergently evolving histone isoforms, also called histone variants, form diverse families that are enriched over distinct features of plant genomes. Among the diverse families of plant histone variants, H2A.Z exclusively marks genes. Here we review recent research progress on the genome-wide distribution patterns and deposition of H2A.Z in plants as well as its association with histone modifications and roles in plant chromatin regulation. We also discuss some hypotheses that explain the different findings about the roles of H2A.Z in plants.
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27
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Fiust A, Rapacz M. Downregulation of three novel candidate genes is important for freezing tolerance of field and laboratory cold acclimated barley. JOURNAL OF PLANT PHYSIOLOGY 2020; 244:153049. [PMID: 31760347 DOI: 10.1016/j.jplph.2019.153049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/25/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Diversity arrays technology (DArT) marker sequences for barley were used for identifying new potential candidate genes for freezing tolerance (FT). We used quantitative trait loci (QTL) genetic linkage maps for FT and photosynthetic acclimation to cold for six- and two-row barley populations, and a set of 20 DArT markers obtained using the association mapping of parameters for photosynthetic acclimation to low temperatures in barley for the bioinformatics analyses. Several nucleotide and amino acid sequence, annotation databases and associated algorithms were used to identify the similarities of six of the marker sequences to potential genes involved in plant low temperature response. Gene ontology (GO) annotations based on similarities to database sequences were assigned to these marker sequences, and indicated potential involvement in signal transduction pathways in response to stress factors and epigenetic processes, as well as auxin transport mechanisms. Furthermore, relative gene expressions for three of six of new identified genes (Hv.ATPase, Hv.DDM1, and Hv.BIG) were assessed within four barley genotypes of different FT. A physiological assessment of FT was conducted based on plant survival rates in two field-laboratory and one laboratory experiments. The results suggested that plant survival rate after freezing but not the degree of freezing-induced leaf damage between the tested accessions can be correlated with the degree of low-temperature downregulation of the studied candidate genes, which encoded proteins involved in the control of plant growth and development. Additionally, candidate genes for qRT-PCR suitable for the analysis of cold acclimation response in barley were suggested after validation.
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Affiliation(s)
- Anna Fiust
- Department of Plant Physiology, University of Agriculture, Podłużna 3, 30-239, Krakow, Poland.
| | - Marcin Rapacz
- Department of Plant Physiology, University of Agriculture, Podłużna 3, 30-239, Krakow, Poland.
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28
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Zhao Z, Li T, Peng X, Wu K, Yang S. Identification and Characterization of Tomato SWI3-Like Proteins: Overexpression of SlSWIC Increases the Leaf Size in Transgenic Arabidopsis. Int J Mol Sci 2019; 20:ijms20205121. [PMID: 31623074 PMCID: PMC6829904 DOI: 10.3390/ijms20205121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
As the subunits of the SWI/SNF (mating-type switching (SWI) and sucrose nonfermenting (SNF)) chromatin-remodeling complexes (CRCs), Swi3-like proteins are crucial to chromatin remodeling in yeast and human. Growing evidence indicate that AtSWI3s are also essential for development and response to hormones in Arabidopsis. Nevertheless, the biological functions of Swi3-like proteins in tomato (Solanum lycopersicum) have not been investigated. Here we identified four Swi3-like proteins from tomato, namely SlSWI3A, SlSWI3B, SlSWI3C, and SlSWI3D. Subcellular localization analysis revealed that all SlSWI3s are localized in the nucleus. The expression patterns showed that all SlSWI3s are ubiquitously expressed in all tissues and organs, and SlSWI3A and SlSWI3B can be induced by cold treatment. In addition, we found that SlSWI3B can form homodimers with itself and heterodimers with SlSWI3A and SlSWI3C. SlSWI3B can also interact with SlRIN and SlCHR8, two proteins involved in tomato reproductive development. Overexpression of SlSWI3C increased the leaf size in transgenic Arabidopsis with increased expression of GROWTH REGULATING FACTORs, such as GRF3, GRF5, and GRF6. Taken together, our results indicate that SlSWI3s may play important roles in tomato growth and development.
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Affiliation(s)
- Zhongyi Zhao
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610064, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- College of Life Sciences, China West Normal University, Nanchong 637002, China.
| | - Tao Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510650, China.
| | - Xiuling Peng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan.
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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29
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Roles of the INO80 and SWR1 Chromatin Remodeling Complexes in Plants. Int J Mol Sci 2019; 20:ijms20184591. [PMID: 31533258 PMCID: PMC6770637 DOI: 10.3390/ijms20184591] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic genes are packed into a dynamic but stable nucleoprotein structure called chromatin. Chromatin-remodeling and modifying complexes generate a dynamic chromatin environment that ensures appropriate DNA processing and metabolism in various processes such as gene expression, as well as DNA replication, repair, and recombination. The INO80 and SWR1 chromatin remodeling complexes (INO80-c and SWR1-c) are ATP-dependent complexes that modulate the incorporation of the histone variant H2A.Z into nucleosomes, which is a critical step in eukaryotic gene regulation. Although SWR1-c has been identified in plants, plant INO80-c has not been successfully isolated and characterized. In this review, we will focus on the functions of the SWR1-c and putative INO80-c (SWR1/INO80-c) multi-subunits and multifunctional complexes in Arabidopsis thaliana. We will describe the subunit compositions of the SWR1/INO80-c and the recent findings from the standpoint of each subunit and discuss their involvement in regulating development and environmental responses in Arabidopsis.
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30
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Rutowicz K, Lirski M, Mermaz B, Teano G, Schubert J, Mestiri I, Kroteń MA, Fabrice TN, Fritz S, Grob S, Ringli C, Cherkezyan L, Barneche F, Jerzmanowski A, Baroux C. Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. Genome Biol 2019; 20:157. [PMID: 31391082 PMCID: PMC6685187 DOI: 10.1186/s13059-019-1767-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/21/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis, while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive. RESULTS We provide a multi-scale functional study of Arabidopsis linker histones. We show that H1-deficient plants are viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation-complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes. CONCLUSIONS H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in Arabidopsis with distinct roles in euchromatin and heterochromatin and a dual causality on gene expression. Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization may contribute to the epigenetic control of developmental and cellular transitions.
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Affiliation(s)
- Kinga Rutowicz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Benoît Mermaz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- Department of Molecular, Cellular & Developmental Biology, Yale University, 352a Osborn memorial laboratories, New Haven, CT, 06511, USA
| | - Gianluca Teano
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Jasmin Schubert
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Imen Mestiri
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Magdalena A Kroteń
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089, Warsaw, Poland
| | - Tohnyui Ndinyanka Fabrice
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Simon Fritz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Stefan Grob
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Christoph Ringli
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Lusik Cherkezyan
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Fredy Barneche
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Célia Baroux
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland.
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A SWI/SNF subunit regulates chromosomal dissociation of structural maintenance complex 5 during DNA repair in plant cells. Proc Natl Acad Sci U S A 2019; 116:15288-15296. [PMID: 31285327 DOI: 10.1073/pnas.1900308116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA damage decreases genome stability and alters genetic information in all organisms. Conserved protein complexes have been evolved for DNA repair in eukaryotes, such as the structural maintenance complex 5/6 (SMC5/6), a chromosomal ATPase involved in DNA double-strand break (DSB) repair. Several factors have been identified for recruitment of SMC5/6 to DSBs, but this complex is also associated with chromosomes under normal conditions; how SMC5/6 dissociates from its original location and moves to DSB sites is completely unknown. In this study, we determined that SWI3B, a subunit of the SWI/SNF complex, is an SMC5-interacting protein in Arabidopsis thialiana Knockdown of SWI3B or SMC5 results in increased DNA damage accumulation. During DNA damage, SWI3B expression is induced, but the SWI3B protein is not localized at DSBs. Notably, either knockdown or overexpression of SWI3B disrupts the DSB recruitment of SMC5 in response to DNA damage. Overexpression of a cotranscriptional activator ADA2b rescues the DSB localization of SMC5 dramatically in the SWI3B-overexpressing cells but only weakly in the SWI3B knockdown cells. Biochemical data confirmed that ADA2b attenuates the interaction between SWI3B and SMC5 and that SWI3B promotes the dissociation of SMC5 from chromosomes. In addition, overexpression of SMC5 reduces DNA damage accumulation in the SWI3B knockdown plants. Collectively, these results indicate that the presence of an appropriate level of SWI3B enhances dissociation of SMC5 from chromosomes for its further recruitment at DSBs during DNA damage in plant cells.
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32
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Kamal KY, Herranz R, van Loon JJWA, Medina FJ. Cell cycle acceleration and changes in essential nuclear functions induced by simulated microgravity in a synchronized Arabidopsis cell culture. PLANT, CELL & ENVIRONMENT 2019; 42:480-494. [PMID: 30105864 DOI: 10.1111/pce.13422] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 07/22/2018] [Accepted: 08/04/2018] [Indexed: 06/08/2023]
Abstract
Zero gravity is an environmental challenge unknown to organisms throughout evolution on Earth. Nevertheless, plants are sensitive to altered gravity, as exemplified by changes in meristematic cell proliferation and growth. We found that synchronized Arabidopsis-cultured cells exposed to simulated microgravity showed a shortened cell cycle, caused by a shorter G2/M phase and a slightly longer G1 phase. The analysis of selected marker genes and proteins by quantitative polymerase chain reaction and flow cytometry in synchronic G1 and G2 subpopulations indicated changes in gene expression of core cell cycle regulators and chromatin-modifying factors, confirming that microgravity induced misregulation of G2/M and G1/S checkpoints and chromatin remodelling. Changes in chromatin-based regulation included higher DNA methylation and lower histone acetylation, increased chromatin condensation, and overall depletion of nuclear transcription. Estimation of ribosome biogenesis rate using nucleolar parameters and selected nucleolar genes and proteins indicated reduced nucleolar activity under simulated microgravity, especially at G2/M. These results expand our knowledge of how meristematic cells are affected by real and simulated microgravity. Counteracting this cellular stress is necessary for plant culture in space exploration.
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Affiliation(s)
- Khaled Y Kamal
- Plant Cell Nucleolus, Proliferation & Microgravity Laboratory, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
- Agronomy Department, Zagazig University, Zagazig, Egypt
| | - Raúl Herranz
- Plant Cell Nucleolus, Proliferation & Microgravity Laboratory, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Jack J W A van Loon
- DESC (Dutch Experiment Support Center), Department of Oral and Maxillofacial Surgery/Oral Pathology, VU University Medical Center and Academic Centre for Dentistry Amsterdam (ACTA), Amsterdam, The Netherlands
- ESA-ESTEC, TEC-MMG, Noordwijk, The Netherlands
| | - F Javier Medina
- Plant Cell Nucleolus, Proliferation & Microgravity Laboratory, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
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33
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Stiller JW, Yang C, Collén J, Kowalczyk N, Thompson BE. Evolution and expression of core SWI/SNF genes in red algae. JOURNAL OF PHYCOLOGY 2018; 54:879-887. [PMID: 30288746 DOI: 10.1111/jpy.12795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Red algae are the oldest identifiable multicellular eukaryotes, with a fossil record dating back more than a billion years. During that time two major rhodophyte lineages, bangiophytes and florideophytes, have evolved varied levels of morphological complexity. These two groups are distinguished, in part, by different patterns of multicellular development, with florideophytes exhibiting a far greater diversity of morphologies. Interestingly, during their long evolutionary history, there is no record of a rhodophyte achieving the kinds of cellular and tissue-specific differentiation present in other multicellular algal lineages. To date, the genetic underpinnings of unique aspects of red algal development are largely unexplored; however, they must reflect the complements and patterns of expression of key regulatory genes. Here we report comparative evolutionary and gene expression analyses of core subunits of the SWI/SNF chromatin-remodeling complex, which is implicated in cell differentiation and developmental regulation in more well studied multicellular groups. Our results suggest that a single, canonical SWI/SNF complex was present in the rhodophyte ancestor, with gene duplications and evolutionary diversification of SWI/SNF subunits accompanying the evolution of multicellularity in the common ancestor of bangiophytes and florideophytes. Differences in how SWI/SNF chromatin remodeling evolved subsequently, in particular gene losses and more rapid divergence of SWI3 and SNF5 in bangiophytes, could help to explain why they exhibit a more limited range of morphological complexity than their florideophyte cousins.
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Affiliation(s)
- John W Stiller
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Chunlin Yang
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Nathalie Kowalczyk
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Beth E Thompson
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
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Yu X, Meng X, Liu Y, Li N, Zhang A, Wang TJ, Jiang L, Pang J, Zhao X, Qi X, Zhang M, Wang S, Liu B, Xu ZY. The chromatin remodeler ZmCHB101 impacts expression of osmotic stress-responsive genes in maize. PLANT MOLECULAR BIOLOGY 2018; 97:451-465. [PMID: 29956114 DOI: 10.1007/s11103-018-0751-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/18/2018] [Indexed: 05/16/2023]
Abstract
The maize chromatin remodeler ZmCHB101 plays an essential role in the osmotic stress response. ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Drought and osmotic stresses are recurring conditions that severely constrain crop production. Evidence accumulated in the model plant Arabidopsis thaliana suggests that core components of SWI/SNF chromatin remodeling complexes play essential roles in abiotic stress responses. However, how maize SWI/SNF chromatin remodeling complexes function in osmotic and drought stress responses remains unknown. Here we show that ZmCHB101, a homolog of A. thaliana SWI3D in maize, plays essential roles in osmotic and dehydration stress responses. ZmCHB101-RNA interference (RNAi) transgenic plants displayed osmotic, salt and drought stress-sensitive phenotypes. Genome-wide RNA-sequencing analysis revealed that ZmCHB101 impacts the transcriptional expression landscape of osmotic stress-responsive genes. Intriguingly, ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Furthermore, we identified that ZmCHB101 associates with RNA polymerase II (RNAPII) in vivo and is a prerequisite for the proper occupancy of RNAPII on the proximal regions of transcription start sites of stress-response genes. Taken together, our findings suggest that ZmCHB101 affects gene expression by remodeling chromatin states and controls RNAPII occupancies in maize under osmotic stress.
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Affiliation(s)
- Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
- Department of Bioengineering, Jilin Agricultural Science and Technology College, Jilin, People's Republic of China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Jinsong Pang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Xinxin Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Xin Qi
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Meishan Zhang
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China.
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35
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Han W, Han D, He Z, Hu H, Wu Q, Zhang J, Jiang J, Qin G, Cui Y, Lai J, Yang C. The SWI/SNF subunit SWI3B regulates IAMT1 expression via chromatin remodeling in Arabidopsis leaf development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:127-132. [PMID: 29650150 DOI: 10.1016/j.plantsci.2018.03.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/03/2018] [Accepted: 03/21/2018] [Indexed: 05/26/2023]
Abstract
The SWI/SNF complex is crucial to chromatin remodeling in various biological processes in different species, but the distinct functions of its components in plant development remain unclear. Here we uncovered the role of SWI3B, a subunit of the Arabidopsis thaliana SWI/SNF complex, via RNA interference. Knockdown of SWI3B resulted in an upward-curling leaf phenotype. Further investigation showed that the RNA level of IAA carboxyl methyltransferase 1 (IAMT1), encoding an enzyme involved in auxin metabolism, was dramatically elevated in the knockdown (SWI3B-RNAi) plants. In addition, activation of IAMT1 produced a leaf-curling phenotype similar to that of the SWI3B-RNAi lines. Database analysis suggested that the last intron of IAMT contains a site of polymerase V (Pol V) stabilized nucleosome, which may be associated with SWI3B. Data from a micrococcal nuclease (MNase) digestion assay showed that nucleosome occupancy around this site was downregulated in the leaves of SWI3B-RNAi plants. In addition, knockdown of IAMT1 in the SWI3B-RNAi background repressed the abnormal leaf development. Thus, SWI3B-mediated chromatin remodeling is critical in regulating the expression of IAMT1 in leaf development.
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Affiliation(s)
- Wenxing Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Zhipeng He
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Huan Hu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Qian Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Juanjuan Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jieming Jiang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, Western University, London, Ontario, Canada
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
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36
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Yolcu S, Li X, Li S, Kim YJ. Beyond the genetic code in leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:801-810. [PMID: 29253191 DOI: 10.1093/jxb/erx401] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
Leaf senescence is not only genetically programmed but also induced by exogenous stress to ensure completion of the plant life cycle, successful reproduction and environmental adaptability. Genetic reprogramming is a major aspect of leaf senescence, and the senescence signaling that follows is controlled by a complex regulatory network. Recent studies suggest that the activity of transcription factors together with epigenetic mechanisms ensures the robustness of this network, with the latter including chromatin remodeling, DNA modification, and RNA-mediated control of transcription factors and other senescence-associated genes. In this review, we provide an overview of the relevant epigenetic mechanisms and summarize recent findings of epigenetic regulators of plant leaf senescence involved in DNA methylation and histone modification along with the functions of small RNAs in this process.
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Affiliation(s)
- Seher Yolcu
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Xiaojie Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shengben Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yun Ju Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
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Ojolo SP, Cao S, Priyadarshani SVGN, Li W, Yan M, Aslam M, Zhao H, Qin Y. Regulation of Plant Growth and Development: A Review From a Chromatin Remodeling Perspective. FRONTIERS IN PLANT SCIENCE 2018; 9:1232. [PMID: 30186301 PMCID: PMC6113404 DOI: 10.3389/fpls.2018.01232] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/03/2018] [Indexed: 05/04/2023]
Abstract
In eukaryotes, genetic material is packaged into a dynamic but stable nucleoprotein structure called chromatin. Post-translational modification of chromatin domains affects the expression of underlying genes and subsequently the identity of cells by conveying epigenetic information from mother to daughter cells. SWI/SNF chromatin remodelers are ATP-dependent complexes that modulate core histone protein polypeptides, incorporate variant histone species and modify nucleotides in DNA strands within the nucleosome. The present review discusses the SWI/SNF chromatin remodeler family, its classification and recent advancements. We also address the involvement of SWI/SNF remodelers in regulating vital plant growth and development processes such as meristem establishment and maintenance, cell differentiation, organ initiation, flower morphogenesis and flowering time regulation. Moreover, the role of chromatin remodelers in key phytohormone signaling pathways is also reviewed. The information provided in this review may prompt further debate and investigations aimed at understanding plant-specific epigenetic regulation mediated by chromatin remodeling under continuously varying plant growth conditions and global climate change.
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Affiliation(s)
- Simon P. Ojolo
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - S. V. G. N. Priyadarshani
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weimin Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Yuan Qin, ;
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38
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Jégu T, Veluchamy A, Ramirez-Prado JS, Rizzi-Paillet C, Perez M, Lhomme A, Latrasse D, Coleno E, Vicaire S, Legras S, Jost B, Rougée M, Barneche F, Bergounioux C, Crespi M, Mahfouz MM, Hirt H, Raynaud C, Benhamed M. The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biol 2017; 18:114. [PMID: 28619072 PMCID: PMC5471679 DOI: 10.1186/s13059-017-1246-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored. RESULTS In this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes. BAF60 binds nucleosome-free regions of multiple G box-containing genes, opposing in cis the promoting effect of the photomorphogenic and thermomorphogenic regulator Phytochrome Interacting Factor 4 (PIF4) on hypocotyl elongation. Furthermore, BAF60 expression level is regulated in response to light and daily rhythms. CONCLUSIONS These results unveil a short path between a chromatin remodeler and a signaling component to fine-tune plant morphogenesis in response to environmental conditions.
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Affiliation(s)
- Teddy Jégu
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Present address: Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Present address: Department of Genetics, Harvard Medical School, Boston, MA, 02114, USA
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan S Ramirez-Prado
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Charley Rizzi-Paillet
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Magalie Perez
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Anaïs Lhomme
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - David Latrasse
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Emeline Coleno
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Serge Vicaire
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Stéphanie Legras
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Bernard Jost
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Martin Rougée
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Fredy Barneche
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Catherine Bergounioux
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Martin Crespi
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Heribert Hirt
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Cécile Raynaud
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France.
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton JM, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M, Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE. Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple. FRONTIERS IN PLANT SCIENCE 2017; 8:1923. [PMID: 29176988 PMCID: PMC5686452 DOI: 10.3389/fpls.2017.01923] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 05/17/2023]
Abstract
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
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Affiliation(s)
- Jorge Urrestarazu
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
- Department of Agricultural Sciences, Public University of Navarre, Pamplona, Spain
- *Correspondence: Jorge Urrestarazu
| | - Hélène Muranty
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Caroline Denancé
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Diane Leforestier
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Elisa Ravon
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Arnaud Guyader
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Rémi Guisnel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Laurence Feugey
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Sébastien Aubourg
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Marc Lateur
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Patrick Houben
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | | | - Jiri Sedlak
- Research and Breeding Institute of Pomology Holovousy Ltd., Horice, Czechia
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | | | | | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | - Charles Poncet
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Anthony Théron
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Shigeki Moriya
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Marco C. A. M. Bink
- Wageningen UR, Biometris, Wageningen, Netherlands
- Hendrix Genetics, Boxmeer, Netherlands
| | - François Laurens
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Charles-Eric Durel
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40
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Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:1058-1070. [PMID: 27549386 DOI: 10.1111/tpj.13312] [Citation(s) in RCA: 437] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 05/18/2023]
Abstract
Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing. The expression of 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open-access web-based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages.
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Affiliation(s)
- Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Artem S Kasianov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny S Gerasimov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Laboratory of Extreme Biology, Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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41
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Buszewicz D, Archacki R, Palusiński A, Kotliński M, Fogtman A, Iwanicka-Nowicka R, Sosnowska K, Kuciński J, Pupel P, Olędzki J, Dadlez M, Misicka A, Jerzmanowski A, Koblowska MK. HD2C histone deacetylase and a SWI/SNF chromatin remodelling complex interact and both are involved in mediating the heat stress response in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:2108-22. [PMID: 27083783 DOI: 10.1111/pce.12756] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/08/2016] [Accepted: 04/10/2016] [Indexed: 05/20/2023]
Abstract
Studies in yeast and animals have revealed that histone deacetylases (HDACs) often act as components of multiprotein complexes, including chromatin remodelling complexes (CRCs). However, interactions between HDACs and CRCs in plants have yet to be demonstrated. Here, we present evidence for the interaction between Arabidopsis HD2C deacetylase and a BRM-containing SWI/SNF CRC. Moreover, we reveal a novel function of HD2C as a regulator of the heat stress response. HD2C transcript levels were strongly induced in plants subjected to heat treatment, and the expression of selected heat-responsive genes was up-regulated in heat-stressed hd2c mutant, suggesting that HD2C acts to down-regulate heat-activated genes. In keeping with the HDAC activity of HD2C, the altered expression of HD2C-regulated genes coincided in most cases with increased histone acetylation at their loci. Microarray transcriptome analysis of hd2c and brm mutants identified a subset of commonly regulated heat-responsive genes, and the effect of the brm hd2c double mutation on the expression of these genes was non-additive. Moreover, heat-treated 3-week-old hd2c, brm and brm hd2c mutants displayed similar rates of growth retardation. Taken together, our findings suggest that HD2C and BRM act in a common genetic pathway to regulate the Arabidopsis heat stress response.
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Affiliation(s)
- Daniel Buszewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland.
| | - Rafał Archacki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106, Warsaw, Poland
| | - Antoni Palusiński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106, Warsaw, Poland
| | - Maciej Kotliński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106, Warsaw, Poland
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106, Warsaw, Poland
| | - Katarzyna Sosnowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Jan Kuciński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106, Warsaw, Poland
| | - Piotr Pupel
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Jacek Olędzki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
- Institute of Genetics and Biotechnology, University of Warsaw, 02-106, Warsaw, Poland
| | - Aleksandra Misicka
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 00-927, Warsaw, Poland
- Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106, Warsaw, Poland
| | - Marta Kamila Koblowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland.
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106, Warsaw, Poland.
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42
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Chen W, Zhu Q, Liu Y, Zhang Q. Chromatin Remodeling and Plant Immunity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 106:243-260. [PMID: 28057214 DOI: 10.1016/bs.apcsb.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense. So what are the links between Snf2-mediated ATP-dependent chromosome remodeling and plant immunity, and what mechanisms might support its involvement in disease resistance?
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Affiliation(s)
- W Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Q Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Y Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Q Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, College of Life Sciences, South China Agricultural University, Guangzhou, China.
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43
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Asensi-Fabado MA, Amtmann A, Perrella G. Plant responses to abiotic stress: The chromatin context of transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:106-122. [PMID: 27487458 DOI: 10.1016/j.bbagrm.2016.07.015] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/09/2016] [Accepted: 07/26/2016] [Indexed: 12/29/2022]
Abstract
The ability of plants to cope with abiotic environmental stresses such as drought, salinity, heat, cold or flooding relies on flexible mechanisms for re-programming gene expression. Over recent years it has become apparent that transcriptional regulation needs to be understood within its structural context. Chromatin, the assembly of DNA with histone proteins, generates a local higher-order structure that impacts on the accessibility and effectiveness of the transcriptional machinery, as well as providing a hub for multiple protein interactions. Several studies have shown that chromatin features such as histone variants and post-translational histone modifications are altered by environmental stress, and they could therefore be primary stress targets that initiate transcriptional stress responses. Alternatively, they could act downstream of stress-induced transcription factors as an integral part of transcriptional activity. A few experimental studies have addressed this 'chicken-and-egg' problem in plants and other systems, but to date the causal relationship between dynamic chromatin changes and transcriptional responses under stress is still unclear. In this review we have collated the existing information on concurrent epigenetic and transcriptional responses of plants to abiotic stress, and we have assessed the evidence using a simple theoretical framework of causality scenarios. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
| | - Anna Amtmann
- Plant Science Group, MCSB, MVLS, University of Glasgow, Glasgow, G128QQ, UK
| | - Giorgio Perrella
- Plant Science Group, MCSB, MVLS, University of Glasgow, Glasgow, G128QQ, UK.
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44
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Sarnowska E, Gratkowska DM, Sacharowski SP, Cwiek P, Tohge T, Fernie AR, Siedlecki JA, Koncz C, Sarnowski TJ. The Role of SWI/SNF Chromatin Remodeling Complexes in Hormone Crosstalk. TRENDS IN PLANT SCIENCE 2016; 21:594-608. [PMID: 26920655 DOI: 10.1016/j.tplants.2016.01.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/14/2015] [Accepted: 01/21/2016] [Indexed: 05/20/2023]
Abstract
SWI/SNF-type ATP-dependent chromatin remodeling complexes (CRCs) are evolutionarily conserved multiprotein machineries controlling DNA accessibility by regulating chromatin structure. We summarize here recent advances highlighting the role of SWI/SNF in the regulation of hormone signaling pathways and their crosstalk in Arabidopsis thaliana. We discuss the functional interdependences of SWI/SNF complexes and key elements regulating developmental and hormone signaling pathways by indicating intriguing similarities and differences in plants and humans, and summarize proposed mechanisms of SWI/SNF action on target loci. We postulate that, given their viability, several plant SWI/SNF mutants may serve as an attractive model for searching for conserved functions of SWI/SNF CRCs in hormone signaling, cell cycle control, and other regulatory pathways.
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Affiliation(s)
| | | | | | - Pawel Cwiek
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Csaba Koncz
- Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany; Institute of Plant Biology, Biological Research Center of Hungarian Academy, Temesvári Körút 62, 6724 Szeged, Hungary
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland.
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45
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Li C, Gu L, Gao L, Chen C, Wei CQ, Qiu Q, Chien CW, Wang S, Jiang L, Ai LF, Chen CY, Yang S, Nguyen V, Qi Y, Snyder MP, Burlingame AL, Kohalmi SE, Huang S, Cao X, Wang ZY, Wu K, Chen X, Cui Y. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nat Genet 2016; 48:687-93. [PMID: 27111034 DOI: 10.1038/ng.3555] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/01/2016] [Indexed: 12/13/2022]
Abstract
SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level, but how they are recruited to specific genomic sites remains largely unknown. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), a plant-unique H3K27 demethylase, targets genomic loci containing a CTCTGYTY motif via its zinc-finger (ZnF) domains and facilitates the recruitment of BRM. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets. Furthermore, REF6 directly binds to the CTCTGYTY motif in vitro, and deletion of the motif from a target gene renders it inaccessible to REF6 in vivo. Finally, we show that, when its ZnF domains are deleted, REF6 loses its genomic targeting ability. Thus, our work identifies a new genomic targeting mechanism for an H3K27 demethylase and demonstrates its key role in recruiting the BRM chromatin remodeler.
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Affiliation(s)
- Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.,Department of Biology, Western University, London, Ontario, Canada
| | - Lianfeng Gu
- Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.,Department of Biology, Western University, London, Ontario, Canada
| | - Chuang-Qi Wei
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.,Life Science College, Hebei Normal University, Shijiazhuang, China
| | - Qi Qiu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chih-Wei Chien
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Suikang Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.,State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Lian-Feng Ai
- Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, China
| | - Chia-Yang Chen
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Yanhua Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | | | - Shangzhi Huang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China.,CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.,Howard Hughes Medical Institute, University of California, Riverside, Riverside, California, USA
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.,Department of Biology, Western University, London, Ontario, Canada
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Peirats-Llobet M, Han SK, Gonzalez-Guzman M, Jeong CW, Rodriguez L, Belda-Palazon B, Wagner D, Rodriguez PL. A Direct Link between Abscisic Acid Sensing and the Chromatin-Remodeling ATPase BRAHMA via Core ABA Signaling Pathway Components. MOLECULAR PLANT 2016; 9:136-147. [PMID: 26499068 DOI: 10.1016/j.molp.2015.10.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 05/04/2023]
Abstract
Optimal response to drought is critical for plant survival and will affect biodiversity and crop performance during climate change. Mitotically heritable epigenetic or dynamic chromatin state changes have been implicated in the plant response to the drought stress hormone abscisic acid (ABA). The Arabidopsis SWI/SNF chromatin-remodeling ATPase BRAHMA (BRM) modulates response to ABA by preventing premature activation of stress response pathways during germination. We show that core ABA signaling pathway components physically interact with BRM and post-translationally modify BRM by phosphorylation/dephosphorylation. Genetic evidence suggests that BRM acts downstream of SnRK2.2/2.3 kinases, and biochemical studies identified phosphorylation sites in the C-terminal region of BRM at SnRK2 target sites that are evolutionarily conserved. Finally, the phosphomimetic BRM(S1760D S1762D) mutant displays ABA hypersensitivity. Prior studies showed that BRM resides at target loci in the ABA pathway in the presence and absence of the stimulus, but is only active in the absence of ABA. Our data suggest that SnRK2-dependent phosphorylation of BRM leads to its inhibition, and PP2CA-mediated dephosphorylation of BRM restores the ability of BRM to repress ABA response. These findings point to the presence of a rapid phosphorylation-based switch to control BRM activity; this property could be potentially harnessed to improve drought tolerance in plants.
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Affiliation(s)
- Marta Peirats-Llobet
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Miguel Gonzalez-Guzman
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Cheol Woong Jeong
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lesia Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Borja Belda-Palazon
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain.
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Abstract
Nucleosome occupancy in promoter and genic regions can severely influence the transcription levels. Few methods have been established to investigate the nucleosome occupancy along the DNA. In this chapter we describe a detailed protocol to analyze the nucleosome occupancy at a specific locus using MNase-pPCR.
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Antosch M, Schubert V, Holzinger P, Houben A, Grasser KD. Mitotic lifecycle of chromosomal 3xHMG-box proteins and the role of their N-terminal domain in the association with rDNA loci and proteolysis. THE NEW PHYTOLOGIST 2015; 208:1067-1077. [PMID: 26213803 DOI: 10.1111/nph.13575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/16/2015] [Indexed: 05/21/2023]
Abstract
The high mobility group (HMG)-box is a DNA-binding domain characteristic of various eukaryotic DNA-binding proteins. 3xHMG-box proteins (containing three copies of the HMG-box domain and a unique basic N-terminal domain) are specific for plants and the Arabidopsis genome encodes two versions termed 3xHMG-box1 and 3xHMG-box2, whose expression is cell cycle-dependent, peaking during mitosis. Here, we analysed in detail the spatiotemporal expression, subcellular localisation and chromosome association of the Arabidopsis thaliana 3xHMG-box proteins. Live cell imaging and structured illumination microscopy revealed that the expression of the 3xHMG-box proteins is induced in late G2 phase of the cell cycle and upon nuclear envelope breakdown in prophase they rapidly associate with the chromosomes. 3xHMG-box1 associates preferentially with 45S rDNA loci and the basic N-terminal domain is involved in the targeting of rDNA loci. Shortly after mitosis the 3xHMG-box proteins are degraded and an N-terminal destruction-box mediates the proteolysis. Ectopic expression/localisation of 3xHMG-box1 in interphase nuclei results in reduced plant growth and various developmental defects including early bolting and abnormal flower morphology. The remarkable conservation of 3xHMG-box proteins within the plant kingdom, their characteristic expression during mitosis, and their striking association with chromosomes, suggest that they play a role in the organisation of plant mitotic chromosomes.
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Affiliation(s)
- Martin Antosch
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466, Stadt Seeland, Germany
| | - Philipp Holzinger
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466, Stadt Seeland, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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49
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Jégu T, Domenichini S, Blein T, Ariel F, Christ A, Kim SK, Crespi M, Boutet-Mercey S, Mouille G, Bourge M, Hirt H, Bergounioux C, Raynaud C, Benhamed M. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture. PLoS One 2015; 10:e0138276. [PMID: 26457678 PMCID: PMC4601769 DOI: 10.1371/journal.pone.0138276] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/26/2015] [Indexed: 02/07/2023] Open
Abstract
Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.
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Affiliation(s)
- Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Séverine Domenichini
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Thomas Blein
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Federico Ariel
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Aurélie Christ
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Soon-Kap Kim
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Martin Crespi
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | | | - Grégory Mouille
- Institut Jean-Pierre Bourgin, UMR1318 INRA/AgroParisTech, Versailles, France
| | - Mickaël Bourge
- Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif, CNRS, IFR87, Gif-sur-Yvette, France
| | - Heribert Hirt
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
- * E-mail:
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50
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Probst AV, Mittelsten Scheid O. Stress-induced structural changes in plant chromatin. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:8-16. [PMID: 26042538 DOI: 10.1016/j.pbi.2015.05.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 05/20/2023]
Abstract
Stress defense in plants is elaborated at the level of protection and adaptation. Dynamic changes in sophisticated chromatin substructures and concomitant transcriptional changes play an important role in response to stress, as illustrated by the transient rearrangement of compact heterochromatin structures or the modulation of chromatin composition and modification upon stress exposure. To connect cytological, developmental, and molecular data around stress and chromatin is currently an interesting, multifaceted, and sometimes controversial field of research. This review highlights some of the most recent findings on nuclear reorganization, histone variants, histone chaperones, DNA- and histone modifications, and somatic and meiotic heritability in connection with stress.
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Affiliation(s)
- Aline V Probst
- CNRS UMR6293 - INSERM U1103 - Clermont University, GReD, Campus Universitaire des Cézeaux, 10 Avenue Blaise Pascal, TSA 60026, CS 60026, 63178 Aubière Cedex, France
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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