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Bente H, Köhler C. Molecular basis and evolutionary drivers of endosperm-based hybridization barriers. PLANT PHYSIOLOGY 2024; 195:155-169. [PMID: 38298124 PMCID: PMC11060687 DOI: 10.1093/plphys/kiae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 02/02/2024]
Abstract
The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.
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Affiliation(s)
- Heinrich Bente
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
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Čermák V, Kašpar T, Fischer L. SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway. FRONTIERS IN PLANT SCIENCE 2024; 15:1372880. [PMID: 38576781 PMCID: PMC10991848 DOI: 10.3389/fpls.2024.1372880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
RNA-directed DNA methylation (RdDM) is driven by small RNAs (sRNAs) complementary to the nascent transcript of RNA polymerase V (Pol V). sRNAs associated with ARGONAUTE (AGO) proteins are tethered to Pol V mainly by the AGO-hook domain of its subunit NRPE1. We found, by in silico analyses, that Pol V strongly colocalizes on chromatin with another AGO-hook protein, SPT6-like (SPT6L), which is a known essential transcription elongation factor of Pol II. Our phylogenetic analysis revealed that SPT6L acquired its AGO-binding capacity already in the most basal streptophyte algae, even before the emergence of Pol V, suggesting that SPT6L might be a driving force behind the RdDM evolution. Since its emergence, SPT6L with the AGO-hook represents the only conserved SPT6 homolog in Viridiplantae, implying that the same protein is involved in both Pol II and Pol V complexes. To better understand the role of SPT6L in the Pol V complex, we characterized genomic loci where these two colocalize and uncovered that DNA methylation there is more dynamic, driven by higher levels of sRNAs often from non-canonical RdDM pathways and more dependent on chromatin modifying and remodeling proteins like MORC. Pol V loci with SPT6L are highly depleted in helitrons but enriched in gene promoters for which locally and temporally precise methylation is necessary. In view of these results, we discuss potential roles of multiple AGO-hook domains present in the Pol V complex and speculate that SPT6L mediates de novo methylation of naïve loci by interconnecting Pol II and Pol V activities.
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Affiliation(s)
- Vojtěch Čermák
- Laboratory of Plant Cell Biology and Biotechnology, Faculty of Science, Department of Experimental Plant Biology, Charles University, Prague, Czechia
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3
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Mahmood T, He S, Abdullah M, Sajjad M, Jia Y, Ahmar S, Fu G, Chen B, Du X. Epigenetic insight into floral transition and seed development in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111926. [PMID: 37984609 DOI: 10.1016/j.plantsci.2023.111926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.
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Affiliation(s)
- Tahir Mahmood
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Muhammad Abdullah
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China.
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4
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Tan Y, Yan X, Sun J, Wan J, Li X, Huang Y, Li L, Niu L, Hou C. Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:234-250. [PMID: 37387536 DOI: 10.1111/tpj.16373] [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: 11/29/2022] [Revised: 05/29/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023]
Abstract
Enhancers are critical cis-regulatory elements controlling gene expression during cell development and differentiation. However, genome-wide enhancer characterization has been challenging due to the lack of a well-defined relationship between enhancers and genes. Function-based methods are the gold standard for determining the biological function of cis-regulatory elements; however, these methods have not been widely applied to plants. Here, we applied a massively parallel reporter assay on Arabidopsis to measure enhancer activities across the genome. We identified 4327 enhancers with various combinations of epigenetic modifications distinctively different from animal enhancers. Furthermore, we showed that enhancers differ from promoters in their preference for transcription factors. Although some enhancers are not conserved and overlap with transposable elements forming clusters, enhancers are generally conserved across thousand Arabidopsis accessions, suggesting they are selected under evolution pressure and could play critical roles in the regulation of important genes. Moreover, comparison analysis reveals that enhancers identified by different strategies do not overlap, suggesting these methods are complementary in nature. In sum, we systematically investigated the features of enhancers identified by functional assay in A. thaliana, which lays the foundation for further investigation into enhancers' functional mechanisms in plants.
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Affiliation(s)
- Yongjun Tan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiaohao Yan
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jialei Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jing Wan
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinxin Li
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yingzhang Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li Li
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longjian Niu
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chunhui Hou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
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Zhu W, Xie Z, Chu Z, Ding Y, Shi G, Chen W, Wei X, Yuan Y, Wei F, Tian B. The Chromatin Remodeling Factor BrCHR39 Targets DNA Methylation to Positively Regulate Apical Dominance in Brassica rapa. PLANTS (BASEL, SWITZERLAND) 2023; 12:1384. [PMID: 36987072 PMCID: PMC10051476 DOI: 10.3390/plants12061384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
The SHPRH (SNF2, histone linker, PHD, RING, helicase) subfamily belonging to ATP-dependent chromatin remodeling factor is the effective tumor-suppressor, which can polyubiquitinate PCNA (proliferating cell nuclear antigen) and participate in post-replication repair in human. However, little is known about the functions of SHPRH proteins in plants. In this study, we identified a novel SHPRH member BrCHR39 and obtained BrCHR39-silenced transgenic Brassica rapa. In contrast to wild-type plants, transgenic Brassica plants exhibited a released apical dominance phenotype with semi-dwarfism and multiple lateral branches. Furthermore, a global alteration of DNA methylation in the main stem and bud appeared after silencing of BrCHR39. Based on the GO (gene ontology) functional annotation and KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis, the plant hormone signal transduction pathway was clearly enriched. In particular, we found a significant increase in the methylation level of auxin-related genes in the stem, whereas auxin- and cytokinin-related genes were hypomethylated in the bud of transgenic plants. In addition, further qRT-PCR (quantitative real-time PCR) analysis revealed that DNA methylation level always had an opposite trend with gene expression level. Considered together, our findings indicated that suppression of BrCHR39 expression triggered the methylation divergence of hormone-related genes and subsequently affected transcription levels to regulate the apical dominance in Brassica rapa.
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Affiliation(s)
- Wei Zhu
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenni Chu
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Yakun Ding
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Gongyao Shi
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Weiwei Chen
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Fang Wei
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Baoming Tian
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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Shang JY, Cai XW, Su YN, Zhang ZC, Wang X, Zhao N, He XJ. Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2438-2454. [PMID: 36354145 DOI: 10.1111/jipb.13406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Although the Trithorax histone methyltransferases ATX1-5 are known to regulate development and stress responses by catalyzing histone H3K4 methylation in Arabidopsis thaliana, it is unknown whether and how these histone methyltransferases affect DNA methylation. Here, we found that the redundant ATX1-5 proteins are not only required for plant development and viability but also for the regulation of DNA methylation. The expression and H3K4me3 levels of both RNA-directed DNA methylation (RdDM) genes (NRPE1, DCL3, IDN2, and IDP2) and active DNA demethylation genes (ROS1, DML2, and DML3) were downregulated in the atx1/2/4/5 mutant. Consistent with the facts that the active DNA demethylation pathway mediates DNA demethylation mainly at CG and CHG sites, and that the RdDM pathway mediates DNA methylation mainly at CHH sites, whole-genome DNA methylation analyses showed that hyper-CG and CHG DMRs in atx1/2/4/5 significantly overlapped with those in the DNA demethylation pathway mutant ros1 dml2 dml3 (rdd), and that hypo-CHH DMRs in atx1/2/4/5 significantly overlapped with those in the RdDM mutant nrpe1, suggesting that the ATX paralogues function redundantly to regulate DNA methylation by promoting H3K4me3 levels and expression levels of both RdDM genes and active DNA demethylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex components function as a whole to regulate DNA methylation. This study reveals a previously uncharacterized mechanism underlying the regulation of DNA methylation.
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Affiliation(s)
- Ji-Yun Shang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Chen Zhang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin Wang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Nan Zhao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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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: 2] [Impact Index Per Article: 1.0] [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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Kundariya H, Sanchez R, Yang X, Hafner A, Mackenzie SA. Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system. Genome Biol 2022; 23:167. [PMID: 35927734 PMCID: PMC9351182 DOI: 10.1186/s13059-022-02731-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Background Plants undergo programmed chromatin changes in response to environment, influencing heritable phenotypic plasticity. The RNA-directed DNA methylation (RdDM) pathway is an essential component of this reprogramming process. The relationship of epigenomic changes to gene networks on a genome-wide basis has been elusive, particularly for intragenic DNA methylation repatterning. Results Epigenomic reprogramming is tractable to detailed study and cross-species modeling in the MSH1 system, where perturbation of the plant-specific gene MSH1 triggers at least four distinct nongenetic states to impact plant stress response and growth vigor. Within this system, we have defined RdDM target loci toward decoding phenotype-relevant methylome data. We analyze intragenic methylome repatterning associated with phenotype transitions, identifying state-specific cytosine methylation changes in pivotal growth-versus-stress, chromatin remodeling, and RNA spliceosome gene networks that encompass 871 genes. Over 77% of these genes, and 81% of their central network hubs, are functionally confirmed as RdDM targets based on analysis of mutant datasets and sRNA cluster associations. These dcl2/dcl3/dcl4-sensitive gene methylation sites, many present as singular cytosines, reside within identifiable sequence motifs. These data reflect intragenic methylation repatterning that is targeted and amenable to prediction. Conclusions A prevailing assumption that biologically relevant DNA methylation variation occurs predominantly in density-defined differentially methylated regions overlooks behavioral features of intragenic, single-site cytosine methylation variation. RdDM-dependent methylation changes within identifiable sequence motifs reveal gene hubs within networks discriminating stress response and growth vigor epigenetic phenotypes. This study uncovers components of a methylome “code” for de novo intragenic methylation repatterning during plant phenotype transitions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02731-w.
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Affiliation(s)
- Hardik Kundariya
- Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA
| | - Robersy Sanchez
- Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA
| | - Xiaodong Yang
- Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA.,School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Alenka Hafner
- Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA.,Plant Biology Graduate Program, The Pennsylvania State University, University Park, PA, USA
| | - Sally A Mackenzie
- Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA. .,Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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Ali S, Khan N, Tang Y. Epigenetic marks for mitigating abiotic stresses in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153740. [PMID: 35716656 DOI: 10.1016/j.jplph.2022.153740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/02/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, FL, 32611, USA
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
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10
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Epigenetic control of abiotic stress signaling in plants. Genes Genomics 2021; 44:267-278. [PMID: 34515950 DOI: 10.1007/s13258-021-01163-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Although plants may be regularly exposed to various abiotic stresses, including drought, salt, cold, heat, heavy metals, and UV-B throughout their lives, it is not possible to actively escape from such stresses due to the immobile nature of plants. To overcome adverse environmental stresses, plants have developed adaptive systems that allow appropriate responses to diverse environmental cues; such responses can be achieved by fine-tuning or controlling genetic and epigenetic regulatory systems. Epigenetic mechanisms such as DNA or histone modifications and modulation of chromatin accessibility have been shown to regulate the expression of stress-responsive genes in struggles against abiotic stresses. OBJECTIVE Herein, the current progress in elucidating the epigenetic regulation of abiotic stress signaling in plants has been summarized in order to further understand the systems plants utilize to effectively respond to abiotic stresses. METHODS This review focuses on the action mechanisms of various components that epigenetically regulate plant abiotic stress responses, mainly in terms of DNA methylation, histone methylation/acetylation, and chromatin remodeling. CONCLUSIONS This review can be considered a basis for further research into understanding the epigenetic control system for abiotic stress responses in plants. Moreover, the knowledge of such systems can be effectively applied in developing novel methods to generate abiotic stress resistant crops.
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Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability. Proc Natl Acad Sci U S A 2021; 118:2107320118. [PMID: 34453006 DOI: 10.1073/pnas.2107320118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeler DDM1 causes hundreds of genomic regions to switch from CMT2 dependency to RdDM dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). Furthermore, we found that dysfunction in both DDM1 and RdDM causes strong reactivation of TEs and a burst of TE transposition in the first generation of mutant plants, indicating that the DDM1 and RdDM pathways together are critical to maintaining TE repression and protecting genomic stability. Our findings reveal the existence of a pathway conversion-based backup mechanism to guarantee the maintenance of DNA methylation and genome integrity.
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Scheid R, Chen J, Zhong X. Biological role and mechanism of chromatin readers in plants. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102008. [PMID: 33581373 PMCID: PMC8222062 DOI: 10.1016/j.pbi.2021.102008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 05/05/2023]
Abstract
Epigenetic modifications are important gene regulatory mechanisms conserved in plants, animals, and fungi. Chromatin reader domains are protein-protein/DNA interaction modules acting within the chromatin-modifying complex to function as molecular interpreters of the epigenetic code. Understanding how reader proteins recognize specific epigenetic modifications and mediate downstream chromatin and transcriptional events is fundamental to many biological processes. Recent studies have uncovered a number of novel reader proteins with diverse functions and mechanisms in plants. Here, we provide an overview of the recent progress on reader-mark recognition modes, the mechanisms by which reader proteins influence chromatin dynamics, and how reader-chromatin interactions regulate biological function. Because of space limitations, this review focuses on reader domains in plants that specifically bind histone methylation, histone acetylation, and DNA methylation.
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Affiliation(s)
- Ray Scheid
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiani Chen
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA.
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13
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Arabidopsis RPD3-like histone deacetylases form multiple complexes involved in stress response. J Genet Genomics 2021; 48:369-383. [PMID: 34144927 DOI: 10.1016/j.jgg.2021.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/31/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022]
Abstract
The Arabidopsis thaliana RPD3-type histone deacetylases have been known to form conserved SIN3-type histone deacetylase complexes, but whether they form other types of complexes is unknown. Here, we perform affinity purification followed by mass spectrometry and demonstrate that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 interact with several previously uncharacterized proteins, thereby forming three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicates that the newly identified components function together with HDA6 and HDA19 and coregulate the expression of a number of genes. HDA6 and HDA19 were previously thought to repress gene transcription by histone deacetylation. We find that the histone deacetylase complexes can repress gene expression via both histone deacetylation-dependent and -independent mechanisms. In the mutants of histone deacetylase complexes, the expression of a number of stress-induced genes is up-regulated, and several mutants of the histone deacetylase complexes show severe retardation in growth. Considering that growth retardation is thought to be a trade-off for an increase in stress tolerance, we infer that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under nonstress conditions.
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14
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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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15
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Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function. PLoS Genet 2020; 16:e1009243. [PMID: 33320854 PMCID: PMC7837471 DOI: 10.1371/journal.pgen.1009243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 01/26/2021] [Accepted: 11/02/2020] [Indexed: 12/22/2022] Open
Abstract
Paramutations represent directed and meiotically-heritable changes in gene regulation leading to apparent violations of Mendelian inheritance. Although the mechanism and evolutionary importance of paramutation behaviors remain largely unknown, genetic screens in maize (Zea mays) identify five components affecting 24 nucleotide RNA biogenesis as required to maintain repression of a paramutant purple plant1 (pl1) allele. Currently, the RNA polymerase IV largest subunit represents the only component also specifying proper development. Here we identify a chromodomain helicase DNA-binding 3 (CHD3) protein orthologous to Arabidopsis (Arabidopsis thaliana) PICKLE as another component maintaining both pl1 paramutation and normal somatic development but without affecting overall small RNA biogenesis. In addition, genetic tests show this protein contributes to proper male gametophyte function. The similar mutant phenotypes documented in Arabidopsis and maize implicate some evolutionarily-conserved gene regulation while developmental defects associated with the two paramutation mutants are largely distinct. Our results show that a CHD3 protein responsible for normal plant ontogeny and sperm transmission also helps maintain meiotically-heritable epigenetic regulatory variation for specific alleles. This finding implicates an intersection of RNA polymerase IV function and nucleosome positioning in the paramutation process. Genes are switched “on” and “off” during normal development by regulating DNA accessibility within the chromosomes. How certain gene variants permanently maintain “off” states from one generation to the next remains unclear, but studies in multiple eukaryotes implicate roles for specific types of small RNAs, some of which define cytosine methylation patterns. In corn, these RNAs come from at least two RNA polymerase II-derived complexes sharing a common catalytic subunit (RPD1). Although RPD1 both controls the normal developmental switching of many genes and permanently maintains some of these “off” states across generations, how RPD1 function defines heritable DNA accessibility is unknown. We discovered that a protein (CHD3a) belonging to a group known to alter nucleosome positioning is also required to help maintain a heritable “off” state for one particular corn gene variant controlling both plant and flower color. We also found CHD3a necessary for normal plant development and sperm transmission consistent with the idea that proper nucleosome positioning defines evolutionarily-important gene expression patterns. Because both CHD3a and RPD1 maintain the heritable “off” state of a specific gene variant, their functions appear to be mechanistically linked.
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Yang R, He L, Huang H, Zhu JK, Lozano-Duran R, Zhang H. RNA-directed DNA methylation has an important developmental function in Arabidopsis that is masked by the chromatin remodeler PICKLE. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1647-1652. [PMID: 32515549 DOI: 10.1111/jipb.12979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
In Arabidopsis, RNA-directed DNA methylation (RdDM) is required for the maintenance of CHH methylation, and for de novo methylation in all (CG, CHG, and CHH) contexts, but no obvious effect of RdDM deficiency on plant development has been found to date. We show that the combination of mutations in the chromatin remodeler PKL and RdDM components results in developmental alterations, which appear in a SUPPRESSOR OF DRM1 DRM2 CMT3 (SDC)-dependent manner.
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Affiliation(s)
- Rong Yang
- Shanghai Center for Plant Stress Biology, Center for Excellence for Molecular Plant Sciences the Chinese Academy of Sciences, Shanghai, 201062, China
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence for Molecular Plant Sciences the Chinese Academy of Sciences, Shanghai, 201062, China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology, Center for Excellence for Molecular Plant Sciences the Chinese Academy of Sciences, Shanghai, 201062, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence for Molecular Plant Sciences the Chinese Academy of Sciences, Shanghai, 201062, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, Center for Excellence for Molecular Plant Sciences the Chinese Academy of Sciences, Shanghai, 201062, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence for Molecular Plant Sciences the Chinese Academy of Sciences, Shanghai, 201062, China
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence for Molecular Plant Sciences the Chinese Academy of Sciences, Shanghai, 200032, China
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17
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Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses. Int J Mol Sci 2020; 21:ijms21207457. [PMID: 33050358 PMCID: PMC7589735 DOI: 10.3390/ijms21207457] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 01/17/2023] Open
Abstract
Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations. Probably, some kind of epigenetic variability underlines environmental adaptation in these cases. Indeed, isogenic plants often have quite variable phenotypes in different habitats. There are examples of successful “invasions” of relatively small and genetically homogenous plant populations into entirely new habitats. The unique capability of quick environmental adaptation appears to be due to a high tendency to transmit epigenetic changes between plant generations. Multiple studies show that epigenetic memory serves as a mechanism of plant adaptation to a rapidly changing environment and, in particular, to aggressive biotic and abiotic stresses. In wild nature, this mechanism underlies, to a very significant extent, plant capability to live in different habitats and endure drastic environmental changes. In agriculture, a deep understanding of this mechanism could serve to elaborate more effective and safe approaches to plant protection.
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18
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Pi T, Liu B, Shi J. Abnormal Homocysteine Metabolism: An Insight of Alzheimer's Disease from DNA Methylation. Behav Neurol 2020; 2020:8438602. [PMID: 32963633 PMCID: PMC7495165 DOI: 10.1155/2020/8438602] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/30/2020] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease in the central nervous system that has complex pathogenesis in the elderly. The current review focuses on the epigenetic mechanisms of AD, according to the latest findings. One of the best-characterized chromatin modifications in epigenetic mechanisms is DNA methylation. Highly replicable data shows that AD occurrence is often accompanied by methylation level changes of the AD-related gene. Homocysteine (Hcy) is not only an intermediate product of one-carbon metabolism but also an important independent risk factor of AD; it can affect the cognitive function of the brain by changing the one-carbon metabolism and interfering with the DNA methylation process, resulting in cerebrovascular disease. In general, Hcy may be an environmental factor that affects AD via the DNA methylation pathway with a series of changes in AD-related substance. This review will concentrate on the relation between DNA methylation and Hcy and try to figure out their rule in the pathophysiology of AD.
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Affiliation(s)
- Tingting Pi
- Department of Pharmacology and the Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Bo Liu
- Department of Pharmacology and the Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Jingshan Shi
- Department of Pharmacology and the Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
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19
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Ruibal C, Castro A, Fleitas AL, Quezada J, Quero G, Vidal S. A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses. FRONTIERS IN PLANT SCIENCE 2020; 11:845. [PMID: 32636864 PMCID: PMC7317016 DOI: 10.3389/fpls.2020.00845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 05/26/2020] [Indexed: 05/17/2023]
Abstract
COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.
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Affiliation(s)
- Cecilia Ruibal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alexandra Castro
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrea L. Fleitas
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Jorge Quezada
- Unidad de Biotecnología Vegetal, Instituto de Biología Molecular y Biotecnología, Carrera de Biología – Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Gastón Quero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Sabina Vidal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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20
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Miao W, Dai J, La Y, Lu C, Zhang J, Hong X, Zhou S, Wang Q, Wang X, Rui Q, Tan F, La H. Characterization and fine mapping of Arabidopsis RLL3, a locus required for DNA demethylation pathway. Mol Genet Genomics 2019; 295:81-93. [PMID: 31486938 DOI: 10.1007/s00438-019-01605-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/13/2019] [Indexed: 01/06/2023]
Abstract
DNA methylation pattern is found to be established by the combined actions of DNA methylation and demethylation. Compared to the DNA methylation pathway, DNA demethylation pathway, however, remains largely unknown. To better understand the DNA demethylation pathway, we performed genetic screening for Arabidopsis mutants with increased genomic DNA methylation levels through a 2 × 35S:LUC (LUC, luciferase) reporter system. A mutant with reduced LUC luminescence was identified by such a system, therefore named rll3-1 (for reduced LUC luminescence 3-1). The rll3-1 mutant exhibited pleiotropic developmental defects, such as delayed bolting as well as flowering, more branches, etc. By map-based cloning approach, rll3 locus that contains a single nuclear recessive mutation as revealed by the genetic analysis was mapped to a region between molecular markers CL102_B1 M1 and CL102_B3M1, which are located in bacterial artificial chromosome (BAC) clones F9P14 and F12K11, respectively, on chromosome 1. Chop-PCR analysis indicated that a total of seven tested loci displayed elevated DNA methylation levels. Whole-genome bisulfite sequencing further revealed 1536 loci exhibiting increased DNA methylation levels relative to Col-LUC control, among which there are 507 such loci overlapping between the rll3-1 and ros1-7 mutants, suggestive of a functional association between RLL3 and REPRESSOR OF SILENCING 1 (ROS1). Further investigations demonstrated that the expression levels of a few genes (like ROS1, IDM1, etc.), which are involved in DNA demethylation pathway, remained unchanged in the rll3-1 mutant, indicating that the increased DNA methylation levels in rll3-1 mutant are not attributable to downregulation of such genes. Taken together, our studies provide a demonstration of the involvement of RLL3 in the DNA demethylation pathway.
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Affiliation(s)
- Wei Miao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jie Dai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yumei La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chong Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jianzhen Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xinyue Hong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaoxia Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiangyu Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qi Rui
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Feng Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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21
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Yang R, Hong Y, Ren Z, Tang K, Zhang H, Zhu JK, Zhao C. A Role for PICKLE in the Regulation of Cold and Salt Stress Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:900. [PMID: 31354770 PMCID: PMC6633207 DOI: 10.3389/fpls.2019.00900] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/26/2019] [Indexed: 05/10/2023]
Abstract
Arabidopsis PICKLE (PKL) is a putative CHD3-type chromatin remodeling factor with important roles in regulating plant growth and development as well as RNA-directed DNA methylation (RdDM). The role of PKL protein in plant abiotic stress response is still poorly understood. Here, we report that PKL is important for cold stress response in Arabidopsis. Loss-of-function mutations in the PKL gene lead to a chlorotic phenotype in seedlings under cold stress, which is caused by the alterations in the transcript levels of some chlorophyll metabolism-related genes. The pkl mutant also exhibits increased electrolyte leakage after freezing treatment. These results suggest that PKL is required for proper chilling and freezing tolerance in plants. Gene expression analysis shows that CBF3, encoding a key transcription factor involved in the regulation of cold-responsive genes, exhibits an altered transcript level in the pkl mutant under cold stress. Transcriptome data also show that PKL regulates the expression of a number of cold-responsive genes, including RD29A, COR15A, and COR15B, possibly through its effect on the expression of CBF3 gene. Mutation in PKL gene also results in decreased cotyledon greening rate and reduced primary root elongation under high salinity. Together, our results suggest that PKL regulates plant responses to cold and salt stress.
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Affiliation(s)
- Rong Yang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Rong Yang,
| | - Yechun Hong
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhizhong Ren
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Kai Tang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Heng Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Kang Zhu
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Chunzhao Zhao
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
- Chunzhao Zhao,
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22
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Susila H, Nasim Z, Ahn JH. Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time. Int J Mol Sci 2018; 19:ijms19103196. [PMID: 30332820 PMCID: PMC6214042 DOI: 10.3390/ijms19103196] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/09/2018] [Accepted: 10/13/2018] [Indexed: 12/23/2022] Open
Abstract
In plants, environmental conditions such as temperature affect survival, growth, and fitness, particularly during key stages such as seedling growth and reproduction. To survive and thrive in changing conditions, plants have evolved adaptive responses that tightly regulate developmental processes such as hypocotyl elongation and flowering time in response to environmental temperature changes. Increases in temperature, coupled with increasing fluctuations in local climate and weather, severely affect our agricultural systems; therefore, understanding the mechanisms by which plants perceive and respond to temperature is critical for agricultural sustainability. In this review, we summarize recent findings on the molecular mechanisms of ambient temperature perception as well as possible temperature sensing components in plants. Based on recent publications, we highlight several temperature response mechanisms, including the deposition and eviction of histone variants, DNA methylation, alternative splicing, protein degradation, and protein localization. We discuss roles of each proposed temperature-sensing mechanism that affects plant development, with an emphasis on flowering time. Studies of plant ambient temperature responses are advancing rapidly, and this review provides insights for future research aimed at understanding the mechanisms of temperature perception and responses in plants.
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Affiliation(s)
- Hendry Susila
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
| | - Zeeshan Nasim
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
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23
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Lepiniec L, Devic M, Roscoe TJ, Bouyer D, Zhou DX, Boulard C, Baud S, Dubreucq B. Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development. PLANT REPRODUCTION 2018; 31:291-307. [PMID: 29797091 DOI: 10.1007/s00497-018-0337-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
The LAFL (i.e. LEC1, ABI3, FUS3, and LEC2) master transcriptional regulators interact to form different complexes that induce embryo development and maturation, and inhibit seed germination and vegetative growth in Arabidopsis. Orthologous genes involved in similar regulatory processes have been described in various angiosperms including important crop species. Consistent with a prominent role of the LAFL regulators in triggering and maintaining embryonic cell fate, their expression appears finely tuned in different tissues during seed development and tightly repressed in vegetative tissues by a surprisingly high number of genetic and epigenetic factors. Partial functional redundancies and intricate feedback regulations of the LAFL have hampered the elucidation of the underpinning molecular mechanisms. Nevertheless, genetic, genomic, cellular, molecular, and biochemical analyses implemented during the last years have greatly improved our knowledge of the LALF network. Here we summarize and discuss recent progress, together with current issues required to gain a comprehensive insight into the network, including the emerging function of LEC1 and possibly LEC2 as pioneer transcription factors.
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Affiliation(s)
- L Lepiniec
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France.
| | - M Devic
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - T J Roscoe
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - D Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - D-X Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Sud 11, Université Paris-Saclay, 91405, Orsay, France
| | - C Boulard
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - S Baud
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - B Dubreucq
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
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Erdmann RM, Satyaki PRV, Klosinska M, Gehring M. A Small RNA Pathway Mediates Allelic Dosage in Endosperm. Cell Rep 2018; 21:3364-3372. [PMID: 29262317 DOI: 10.1016/j.celrep.2017.11.078] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/18/2017] [Accepted: 11/21/2017] [Indexed: 12/12/2022] Open
Abstract
Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here, we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24-nt small RNAs are reduced in transposable elements and enriched in genes compared with the embryo. We find an inverse relationship between the parent of origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates the transcriptional balance between maternally and paternally inherited genomes in endosperm.
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Affiliation(s)
- Robert M Erdmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Maja Klosinska
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Zhang M, Liu XK, Fan W, Yan DF, Zhong NS, Gao JY, Zhang WJ. Transcriptome analysis reveals hybridization-induced genome shock in an interspecific F 1 hybrid from Camellia. Genome 2018; 61:477-485. [PMID: 29718690 DOI: 10.1139/gen-2017-0105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The combination of two divergent genomes during hybridization can result in "genome shock". Although genome shock has been reported in the hybrids of some herbaceous plants, the pattern and the principle it follows are far from understood, especially in woody plants. Here, the gene expression patterns were remodeled in the F1 hybrid from the crossing of Camellia azalea × Camellia amplexicaulis compared with the parents as revealed by RNA-seq. About 54.5% of all unigenes were differentially expressed between the F1 hybrid and at least one of the parents, including 6404 unigenes with the highest expression level in the F1 hybrid. A series of genes, related to flower development, essential for RNA-directed DNA methylation and histone methylation, as well as 223 transposable elements, were enriched; and most of them exhibited a higher level of expression in the F1 hybrid. These results indicated that the genome shock induced by interspecific hybridization in Camellia could indeed result in changes of gene expression patterns, potentially through regulating DNA methylation and histone methylation which may be helpful for the maintaining of genome stability and even related to the unique phenotype of the F1 hybrid.
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Affiliation(s)
- Min Zhang
- a Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin-Kai Liu
- b Palm Eco-Town Development Co., Ltd., Guangzhou, Guangdong 510627, China
| | - Wen Fan
- a Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Dan-Feng Yan
- b Palm Eco-Town Development Co., Ltd., Guangzhou, Guangdong 510627, China
| | - Nai-Sheng Zhong
- b Palm Eco-Town Development Co., Ltd., Guangzhou, Guangdong 510627, China
| | - Ji-Yin Gao
- b Palm Eco-Town Development Co., Ltd., Guangzhou, Guangdong 510627, China.,c Research Institute of Subtropical Forest, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Wen-Ju Zhang
- a Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
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Grover JW, Kendall T, Baten A, Burgess D, Freeling M, King GJ, Mosher RA. Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:575-582. [PMID: 29569777 DOI: 10.1111/tpj.13910] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 03/10/2018] [Accepted: 03/13/2018] [Indexed: 05/20/2023]
Abstract
Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction. Here we show that, unlike Arabidopsis, mutations in the Pol IV-dependent small RNA pathway cause severe and specific reproductive defects in Brassica rapa. High rates of abortion occur when seeds have RdDM mutant mothers, but not when they have mutant fathers. Although abortion occurs after fertilization, RdDM function is required in maternal somatic tissue, not in the female gametophyte or the developing zygote, suggesting that siRNAs from the maternal soma might function in filial tissues. We propose that recently outbreeding species such as B. rapa are key to understanding the role of RdDM during plant reproduction.
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Affiliation(s)
- Jeffrey W Grover
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Timmy Kendall
- The School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Diane Burgess
- Department of Plant and Microbial Biology, The University of California, Berkeley, CA, 94720, USA
| | - Michael Freeling
- Department of Plant and Microbial Biology, The University of California, Berkeley, CA, 94720, USA
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Rebecca A Mosher
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ, 85721, USA
- The School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
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27
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Köhler C, Springer N. Plant epigenomics-deciphering the mechanisms of epigenetic inheritance and plasticity in plants. Genome Biol 2017; 18:132. [PMID: 28683755 PMCID: PMC5501107 DOI: 10.1186/s13059-017-1260-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Claudia Köhler
- Uppsala BioCenter, Department of Plant Biology and Forest Genetics, The Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Almas Allé 5, SE-750 07, Uppsala, Sweden.
| | - Nathan Springer
- College of Biological Sciences, University of Minnesota, 306 Biological Sciences, 1445 Gortner Avenue, St Paul, MN, 55108, USA.
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