1
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Wang X, Yamaguchi N. Cause or effect: Probing the roles of epigenetics in plant development and environmental responses. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102569. [PMID: 38833828 DOI: 10.1016/j.pbi.2024.102569] [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: 01/25/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
Epigenetic modifications are inheritable, reversible changes that control gene expression without altering the DNA sequence itself. Recent advances in epigenetic and sequencing technologies have revealed key regulatory regions in genes with multiple epigenetic changes. However, causal associations between epigenetic changes and physiological events have rarely been examined. Epigenome editing enables alterations to the epigenome without changing the underlying DNA sequence. Modifying epigenetic information in plants has important implications for causality assessment of the epigenome. Here, we briefly review tools for selectively interrogating the epigenome. We highlight promising research on site-specific DNA methylation and histone modifications and propose future research directions to more deeply investigate epigenetic regulation, including cause-and-effect relationships between epigenetic modifications and the development/environmental responses of Arabidopsis thaliana.
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Affiliation(s)
- Xuejing Wang
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
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2
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Haider S, Farrona S. Decoding histone 3 lysine methylation: Insights into seed germination and flowering. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102598. [PMID: 38986392 DOI: 10.1016/j.pbi.2024.102598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/01/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
Histone lysine methylation is a highly conserved epigenetic modification across eukaryotes that contributes to creating different dynamic chromatin states, which may result in transcriptional changes. Over the years, an accumulated set of evidence has shown that histone methylation allows plants to align their development with their surroundings, enabling them to respond and memorize past events due to changes in the environment. In this review, we discuss the molecular mechanisms of histone methylation in plants. Writers, readers, and erasers of Arabidopsis histone methylation marks are described with an emphasis on their role in two of the most important developmental transition phases in plants, seed germination and flowering. Further, the crosstalk between different methylation marks is also discussed. An overview of the mechanisms of histone methylation modifications and their biological outcomes will shed light on existing research gaps and may provide novel perspectives to increase crop yield and resistance in the era of global climate change.
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Affiliation(s)
- Saqlain Haider
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland.
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3
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Li W, Zhang X, Zhang Q, Li Q, Li Y, Lv Y, Liu Y, Cao Y, Wang H, Chen X, Yang H. PICKLE and HISTONE DEACETYLASE6 coordinately regulate genes and transposable elements in Arabidopsis. PLANT PHYSIOLOGY 2024; 196:1080-1094. [PMID: 38976580 DOI: 10.1093/plphys/kiae369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024]
Abstract
Chromatin dynamics play essential roles in transcriptional regulation. The chromodomain helicase DNA-binding domain 3 chromatin remodeler PICKLE (PKL) and HISTONE DEACETYLASE6 (HDA6) are required for transcriptional gene silencing, but their coordinated function in gene repression requires further study. Through a genetic suppressor screen, we found that a point mutation at PKL could partially restore the developmental defects of a weak Polycomb repressive complex 1 (PRC1) mutant (ring1a-2 ring1b-3), in which RING1A expression is suppressed by a T-DNA insertion at the promoter. Compared to ring1a-2 ring1b-3, the expression of RING1A is increased, nucleosome occupancy is reduced, and the histone 3 lysine 9 acetylation (H3K9ac) level is increased at the RING1A locus in the pkl ring1a-2 ring1b-3 triple mutant. HDA6 interacts with PKL and represses RING1A expression similarly to PKL genetically and molecularly in the ring1a-2 ring1b-3 background. Furthermore, we show that PKL and HDA6 suppress the expression of a set of genes and transposable elements (TEs) by increasing nucleosome density and reducing H3K9ac. Genome-wide analysis indicated they possibly coordinately maintain DNA methylation as well. Our findings suggest that PKL and HDA6 function together to reduce H3K9ac and increase nucleosome occupancy, thereby facilitating gene/TE regulation in Arabidopsis (Arabidopsis thaliana).
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Affiliation(s)
- Wenjuan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
| | - Xiaoling Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Cotton Research Institute, Shanxi Agricultural University, Yuncheng 044000, China
| | - Qingche Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
| | - Qingzhu Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
| | - Yanzhuo Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
| | - Yanfang Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
| | - Yue Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
| | - Ying Cao
- College of Life Sciences, RNA Center, Capital Normal University, Beijing 100048, China
| | - Huamei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
- RNA Institute, Wuhan University, Wuhan 430072, China
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4
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Guo J, He XJ. Composition and function of plant chromatin remodeling complexes. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102613. [PMID: 39116678 DOI: 10.1016/j.pbi.2024.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/10/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024]
Abstract
ATP-dependent chromatin remodelers play a crucial role in modifying chromatin configuration by utilizing the energy of ATP hydrolysis. They are involved in various processes, including transcription, DNA replication, and maintaining genome stability. These remodeling remodelers usually form multi-subunit chromatin remodeling complexes in eukaryotes. In plants, chromatin remodeling complexes have diverse functions in regulating plant development and stress response. Recent studies have conducted extensive research on plant chromatin remodeling complexes. This review focuses on recent advances in the classification and composition of plant chromatin remodeling complexes, the protein-protein interactions within the complexes, their impact on chromatin configuration, and their interactions with chromatin modifications and transcription factors.
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Affiliation(s)
- Jing Guo
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China.
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5
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Rudolf J, Tomovicova L, Panzarova K, Fajkus J, Hejatko J, Skalak J. Epigenetics and plant hormone dynamics: a functional and methodological perspective. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5267-5294. [PMID: 38373206 PMCID: PMC11389840 DOI: 10.1093/jxb/erae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.
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Affiliation(s)
- Jiri Rudolf
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Lucia Tomovicova
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Klara Panzarova
- Photon Systems Instruments, Prumyslova 470, CZ-664 24 Drasov, Czech Republic
| | - Jiri Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Jan Hejatko
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Jan Skalak
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
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6
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Wang Q, Wang L, Cheng H, Wang S, Li J, Zhang D, Zhou L, Chen S, Chen F, Jiang J. Two B-box proteins orchestrate vegetative and reproductive growth in summer chrysanthemum. PLANT, CELL & ENVIRONMENT 2024; 47:2923-2935. [PMID: 38629334 DOI: 10.1111/pce.14919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/23/2024] [Accepted: 04/05/2024] [Indexed: 07/12/2024]
Abstract
Floral transition, the switch from vegetative to reproductive growth, is extremely important for the growth and development of flowering plants. In the summer chrysanthemum, CmBBX8, a member of the subgroup II B-box (BBX) family, positively regulates the transition by physically interacting with CmERF3 to inhibit CmFTL1 expression. In this study, we show that CmBBX5, a B-box subgroup I member comprising two B-boxes and a CCT domain, interacts with CmBBX8. This interaction suppresses the recruitment of CmBBX8 to the CmFTL1 locus without affecting its transcriptional activation activity. CmBBX5 overexpression led to delayed flowering under both LD (long-day) and SD (short-day) conditions, while lines expressing the chimeric repressor gene-silencing (CmBBX5-SRDX) exhibited the opposite phenotype. Subsequent genetic evidence indicated that in regulating flowering, CmBBX5 is partially dependent on CmBBX8. Moreover, during the vegetative growth period, levels of CmBBX5 expression were found to exceed those of CmBBX8. Collectively, our findings indicate that both CmERF3 and CmBBX5 interact with CmBBX8 to dampen the regulation of CmFTL1 via distinct mechanisms, which contribute to preventing the premature flowering of summer chrysanthemum.
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Affiliation(s)
- Qi Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lijun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hua Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shuang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiayu Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Deng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lijie Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilisation, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Zhongshan Biological Breeding Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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7
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Plskova Z, Van Breusegem F, Kerchev P. Redox regulation of chromatin remodelling in plants. PLANT, CELL & ENVIRONMENT 2024; 47:2780-2792. [PMID: 38311877 DOI: 10.1111/pce.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/23/2023] [Accepted: 01/22/2024] [Indexed: 02/06/2024]
Abstract
Changes in the cellular redox balance that occur during plant responses to unfavourable environmental conditions significantly affect a myriad of redox-sensitive processes, including those that impact on the epigenetic state of the chromatin. Various epigenetic factors, like histone modifying enzymes, chromatin remodelers, and DNA methyltransferases can be targeted by oxidative posttranslational modifications. As their combined action affects the epigenetic regulation of gene expression, they form an integral part of plant responses to (a)biotic stress. Epigenetic changes triggered by unfavourable environmental conditions are intrinsically linked with primary metabolism that supplies intermediates and donors, such acetyl-CoA and S-adenosyl-methionine, that are critical for the epigenetic decoration of histones and DNA. Here, we review the recent advances in our understanding of redox regulation of chromatin remodelling, dynamics of epigenetic marks, and the interplay between epigenetic control of gene expression, redox signalling and primary metabolism within an (a)biotic stress context.
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Affiliation(s)
- Zuzana Plskova
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Frank Van Breusegem
- VIB Center of Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, UGent, Ghent, Belgium
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
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8
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Poethig RS, Fouracre J. Temporal regulation of vegetative phase change in plants. Dev Cell 2024; 59:4-19. [PMID: 38194910 PMCID: PMC10783531 DOI: 10.1016/j.devcel.2023.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.
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Affiliation(s)
- R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jim Fouracre
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
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9
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Nguyen NH, Sng BJR, Chin HJ, Choi IKY, Yeo HC, Jang IC. HISTONE DEACETYLASE 9 promotes hypocotyl-specific auxin response under shade. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:804-822. [PMID: 37522556 DOI: 10.1111/tpj.16410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Vegetative shade causes an array of morphological changes in plants called shade avoidance syndrome, which includes hypocotyl and petiole elongation, leaf hyponasty, reduced leaf growth, early flowering and rapid senescence. Here, we show that loss-of-function mutations in HISTONE DEACETYLASE 9 (HDA9) attenuated the shade-induced hypocotyl elongation in Arabidopsis. However, the hda9 cotyledons and petioles under shade were not significantly different from those in wild-type, suggesting a specific function of HDA9 in hypocotyl elongation in response to shade. HDA9 expression levels were stable under shade and its protein was ubiquitously detected in cotyledon, hypocotyl and root. Organ-specific transcriptome analysis unraveled that shade induced a set of auxin-responsive genes, such as SMALL AUXIN UPREGULATED RNAs (SAURs) and AUXIN/INDOLE-3-ACETIC ACIDs (AUX/IAAs) and their induction was impaired in hda9-1 hypocotyls. In addition, HDA9 binding to loci of SAUR15/65, IAA5/6/19 and ACS4 was increased under shade. The genetic and organ-specific gene expression analyses further revealed that HDA9 may cooperate with PHYTOCHROME-INTERACTING FACTOR 4/7 in the regulation of shade-induced hypocotyl elongation. Furthermore, HDA9 and PIF7 proteins were found to interact together and thus it is suggested that PIF7 may recruit HDA9 to regulate the shade/auxin responsive genes in response to shade. Overall, our study unravels that HDA9 can work as one component of a hypocotyl-specific transcriptional regulatory machinery that activates the auxin response at the hypocotyl leading to the elongation of this organ under shade.
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Affiliation(s)
- Nguyen Hoai Nguyen
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Benny Jian Rong Sng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Hui Jun Chin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Ian Kin Yuen Choi
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Hock Chuan Yeo
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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10
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Pei LL, Zhang LL, Liu X, Jiang J. Role of microRNA miR171 in plant development. PeerJ 2023; 11:e15632. [PMID: 37456878 PMCID: PMC10340099 DOI: 10.7717/peerj.15632] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19-24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both "GAGCCG" and "CAAUAU" fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171's target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.
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Affiliation(s)
- Ling Ling Pei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Ling Ling Zhang
- College of Horticulture, Shenyang Agriculture University, Shenyang, Shenhe District, China
| | - Xin Liu
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Jing Jiang
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
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11
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Jing Y, Yang Z, Yang R, Zhang Y, Qiao W, Zhou Y, Sun J. PKL is stabilized by MMS21 to negatively regulate Arabidopsis drought tolerance through directly repressing AFL1 transcription. THE NEW PHYTOLOGIST 2023. [PMID: 37209253 DOI: 10.1111/nph.18972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/20/2023] [Indexed: 05/22/2023]
Abstract
Drought stress causes substantial losses in crop production per year worldwide, threatening global food security. Identification of the genetic components underlying drought tolerance in plants is of great importance. In this study, we report that loss-of-function of the chromatin-remodeling factor PICKLE (PKL), which is involved in repression of transcription, enhances drought tolerance of Arabidopsis. At first, we find that PKL interacts with ABI5 to regulate seed germination, but PKL regulates drought tolerance independently of ABI5. Then, we find that PKL is necessary for repressing the drought-tolerant gene AFL1, which is responsible for the drought-tolerant phenotype of pkl mutant. Genetic complementation tests demonstrate that the Chromo domain and ATPase domain but not the PHD domain are required for the function of PKL in regulating drought tolerance. Interestingly, we find that the DNA-binding domain (DBD) is essential for the protein stability of PKL. Furthermore, we demonstrate that the SUMO E3 ligase MMS21 interacts with and enhances the protein stability of PKL. Genetic interaction analysis shows that MMS21 and PKL additively regulate plant drought tolerance. Collectively, our findings uncover a MMS21-PKL-AFL1 module in regulating plant drought tolerance and offer insights into a novel strategy to improve crop drought tolerance.
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Affiliation(s)
- Yexing Jing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ziyi Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruizhen Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunwei Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Qiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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12
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Liang Z, Yuan L, Xiong X, Hao Y, Song X, Zhu T, Yu Y, Fu W, Lei Y, Xu J, Liu J, Li JF, Li C. The transcriptional repressors VAL1 and VAL2 mediate genome-wide recruitment of the CHD3 chromatin remodeler PICKLE in Arabidopsis. THE PLANT CELL 2022; 34:3915-3935. [PMID: 35866997 PMCID: PMC9516181 DOI: 10.1093/plcell/koac217] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 05/30/2023]
Abstract
PICKLE (PKL) is a chromodomain helicase DNA-binding domain 3 (CHD3) chromatin remodeler that plays essential roles in controlling the gene expression patterns that determine developmental identity in plants, but the molecular mechanisms through which PKL is recruited to its target genes remain elusive. Here, we define a cis-motif and trans-acting factors mechanism that governs the genomic occupancy profile of PKL in Arabidopsis thaliana. We show that two homologous trans-factors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 physically interact with PKL in vivo, localize extensively to PKL-occupied regions in the genome, and promote efficient PKL recruitment at thousands of target genes, including those involved in seed maturation. Transcriptome analysis and genetic interaction studies reveal a close cooperation of VAL1/VAL2 and PKL in regulating gene expression and developmental fate. We demonstrate that this recruitment operates at two master regulatory genes, ABSCISIC ACID INSENSITIVE3 and AGAMOUS-LIKE 15, to repress the seed maturation program and ensure the seed-to-seedling transition. Together, our work unveils a general rule through which the CHD3 chromatin remodeler PKL binds to its target chromatin in plants.
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Affiliation(s)
- Zhenwei Liang
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbing Yuan
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangyu Xiong
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuanhao Hao
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tao Zhu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yawen Lei
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jianqu Xu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jian-Feng Li
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
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