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Chromatin, Epigenetics and Plant Physiology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (29 November 2019) | Viewed by 42504

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Special Issue Editors

Mendel Centre for Plant Genomics and Proteomics, Masaryk University, Brno, Czech Republic
Interests: telomeres; telomerase; chromatin; epigenetics; genome stability; DNA repair; plant molecular biology
Special Issues, Collections and Topics in MDPI journals
Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
Interests: chromatin; epigenetics; plant molecular biology; telomeres; telomerase; DNA methylation; histone posttranslational modifications
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We would like to invite you to contribute to this Special Issue of IJMS on “Chromatin, Epigenetics and Plant Physiology”. This SI will focus on current progress in understanding the role of chromatin structure and its modifications. The interest in this topic follows from the fact that eukaryotic genomes are packed into the supramolecular nucleoprotein structure of chromatin. Therefore, our understanding of processes such as DNA replication and repair, transcription or cell differentiation requires understanding the structure and function of chromatin, and its specific domains like centromeres, telomeres or rDNA loci.

While the nucleotide sequence of the DNA component of chromatin constitutes the genetic material of the cell, the other chromatin components (and also modifications of bases in the DNA itself) participate in so-called epigenetic processes. These processes are essential, e.g., in cell differentiation and ontogenesis, or adaptation to changes in the environment. Therefore, epigenetics is particularly important (and elaborated) in plants that show a high developmental plasticity and, as sessile organisms, display an enormous capacity to cope with environmental stress. In these processes, epigenetic mechanisms show crosstalk with plant signalling pathways mediated by phytohormones. Current advances in methodological tools has made it possible to investigate chromatin structure starting from its basic level, the nucleosome, up to the higher-order structures (chromatin fibres, topologically associated domains, chromosome territories), and their dynamics associated with the differentiation and physiological status of cells. Thus, we aim to offer representative examples of research progress in this broad research field in this IJMS Special Issue, and invite original, methodology and review contributions on this hot topic in plant sciences.

Prof. Dr. Jiří Fajkus
Prof. Dr. Miloslava Fojtová
Guest Editors

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Keywords

  • chromatin organisation, assembly and remodelling
  • nucleosome
  • epigenetics
  • DNA methylation
  • histone variants and posttranslational modifications
  • methods
  • regulatory RNAs

Published Papers (11 papers)

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Editorial

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3 pages, 201 KiB  
Editorial
Chromatin, Epigenetics and Plant Physiology
Int. J. Mol. Sci. 2020, 21(8), 2763; https://doi.org/10.3390/ijms21082763 - 16 Apr 2020
Cited by 3 | Viewed by 1941
Abstract
The ever-increasing interest in epigenetics comes from the fact that in the diverse life situations of organisms, e [...] Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)

Research

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15 pages, 3824 KiB  
Article
The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE
Int. J. Mol. Sci. 2020, 21(7), 2373; https://doi.org/10.3390/ijms21072373 - 30 Mar 2020
Cited by 6 | Viewed by 3340
Abstract
The integration of T-DNA in plant genomes is widely used for basic research and agriculture. The high heterogeneity in the number of integration events per genome, their configuration, and their impact on genome integrity highlight the critical need to detect the genomic locations [...] Read more.
The integration of T-DNA in plant genomes is widely used for basic research and agriculture. The high heterogeneity in the number of integration events per genome, their configuration, and their impact on genome integrity highlight the critical need to detect the genomic locations of T-DNA insertions and their associated chromosomal rearrangements, and the great challenge in doing so. Here, we present 4SEE, a circular chromosome conformation capture (4C)-based method for robust, rapid, and cost-efficient detection of the entire scope of T-DNA locations. Moreover, by measuring the chromosomal architecture of the plant genome flanking the T-DNA insertions, 4SEE outlines their associated complex chromosomal aberrations. Applying 4SEE to a collection of confirmed T-DNA lines revealed previously unmapped T-DNA insertions and chromosomal rearrangements such as inversions and translocations. Uncovering such events in a feasible, robust, and cost-effective manner by 4SEE in any plant of interest has implications for accurate annotation and phenotypic characterization of T-DNA insertion mutants and transgene expression in basic science applications as well as for plant biotechnology. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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16 pages, 6755 KiB  
Article
Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana
Int. J. Mol. Sci. 2020, 21(3), 792; https://doi.org/10.3390/ijms21030792 - 25 Jan 2020
Cited by 19 | Viewed by 2784
Abstract
Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3′–5′ ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of [...] Read more.
Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3′–5′ ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. However, the roles of circRNAs in the JA regulatory network are unclear. In this study, we performed high-throughput sequencing of Arabidopsis thaliana at 24 h, 48 h, and 96 h after methyl JA (MeJA) treatment. A total of 8588 circRNAs, which were distributed on almost all chromosomes, were identified, and the majority of circRNAs had lengths between 200 and 800 bp. We identified 385 differentially expressed circRNAs (DEcircRNAs) by comparing data between MeJA-treated and untreated samples. Gene Ontology (GO) enrichment analysis of the host genes that produced the DEcircRNAs showed that the DEcircRNAs are mainly involved in response to stimulation and metabolism. Additionally, some DEcircRNAs were predicted to act as miRNA decoys. Eight DEcircRNAs were validated by qRT-PCR with divergent primers, and the junction sites of five DEcircRNAs were validated by PCR analysis and Sanger sequencing. Our results provide insight into the potential roles of circRNAs in the MeJA regulation network. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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19 pages, 3511 KiB  
Article
The SWI/SNF ATP-Dependent Chromatin Remodeling Complex in Arabidopsis Responds to Environmental Changes in Temperature-Dependent Manner
Int. J. Mol. Sci. 2020, 21(3), 762; https://doi.org/10.3390/ijms21030762 - 23 Jan 2020
Cited by 11 | Viewed by 4547
Abstract
SWI/SNF ATP-dependent chromatin remodeling complexes (CRCs) play important roles in the regulation of transcription, cell cycle, DNA replication, repair, and hormone signaling in eukaryotes. The core of SWI/SNF CRCs composed of a SWI2/SNF2 type ATPase, a SNF5 and two of SWI3 subunits is [...] Read more.
SWI/SNF ATP-dependent chromatin remodeling complexes (CRCs) play important roles in the regulation of transcription, cell cycle, DNA replication, repair, and hormone signaling in eukaryotes. The core of SWI/SNF CRCs composed of a SWI2/SNF2 type ATPase, a SNF5 and two of SWI3 subunits is sufficient for execution of nucleosome remodeling in vitro. The Arabidopsis genome encodes four SWI2/SNF2 ATPases, four SWI3, a single SNF5 and two SWP73 subunits. Genes of the core SWI/SNF components have critical but not fully overlapping roles during plant growth, embryogenesis, and sporophyte development. Here we show that the Arabidopsis swi3c mutant exhibits a phenotypic reversion when grown at lower temperature resulting in partial restoration of its embryo, root development and fertility defects. Our data indicates that the swi3c mutation alters the expression of several genes engaged in low temperature responses. The location of SWI3C-containing SWI/SNF CRCs on the ICE1, MYB15 and CBF1 target genes depends on the temperature conditions, and the swi3c mutation thus also influences the transcription of several cold-responsive (COR) genes. These findings, together with genetic analysis of swi3c/ice1 double mutant and enhanced freezing tolerance of swi3c plants illustrate that SWI/SNF CRCs contribute to fine-tuning of plant growth responses to different temperature regimes. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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19 pages, 2296 KiB  
Article
Depletion of KNL2 Results in Altered Expression of Genes Involved in Regulation of the Cell Cycle, Transcription, and Development in Arabidopsis
Int. J. Mol. Sci. 2019, 20(22), 5726; https://doi.org/10.3390/ijms20225726 - 15 Nov 2019
Cited by 4 | Viewed by 3803
Abstract
Centromeres contain specialized nucleosomes at which histone H3 is partially replaced by the centromeric histone H3 variant cenH3 that is required for the assembly, maintenance, and proper function of kinetochores during mitotic and meiotic divisions. Previously, we identified a KINETOCHORE NULL 2 (KNL2) [...] Read more.
Centromeres contain specialized nucleosomes at which histone H3 is partially replaced by the centromeric histone H3 variant cenH3 that is required for the assembly, maintenance, and proper function of kinetochores during mitotic and meiotic divisions. Previously, we identified a KINETOCHORE NULL 2 (KNL2) of Arabidopsis thaliana that is involved in the licensing of centromeres for the cenH3 recruitment. We also demonstrated that a knockout mutant for KNL2 shows mitotic and meiotic defects, slower development, reduced growth rate, and fertility. To analyze an effect of KNL2 mutation on global gene transcription of Arabidopsis, we performed RNA-sequencing experiments using seedling and flower bud tissues of knl2 and wild-type plants. The transcriptome data analysis revealed a high number of differentially expressed genes (DEGs) in knl2 plants. The set was enriched in genes involved in the regulation of the cell cycle, transcription, development, and DNA damage repair. In addition to comprehensive information regarding the effects of KNL2 mutation on the global gene expression, physiological changes in plants are also presented, which provides an integrated understanding of the critical role played by KNL2 in plant growth and development. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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17 pages, 3263 KiB  
Article
Identification and Characterization of Tomato SWI3-Like Proteins: Overexpression of SlSWIC Increases the Leaf Size in Transgenic Arabidopsis
Int. J. Mol. Sci. 2019, 20(20), 5121; https://doi.org/10.3390/ijms20205121 - 16 Oct 2019
Cited by 7 | Viewed by 2571
Abstract
As the subunits of the SWI/SNF (mating-type switching (SWI) and sucrose nonfermenting (SNF)) chromatin-remodeling complexes (CRCs), Swi3-like proteins are crucial to chromatin remodeling in yeast and human. Growing evidence indicate that AtSWI3s are also essential for development and response to hormones in Arabidopsis [...] Read more.
As the subunits of the SWI/SNF (mating-type switching (SWI) and sucrose nonfermenting (SNF)) chromatin-remodeling complexes (CRCs), Swi3-like proteins are crucial to chromatin remodeling in yeast and human. Growing evidence indicate that AtSWI3s are also essential for development and response to hormones in Arabidopsis. Nevertheless, the biological functions of Swi3-like proteins in tomato (Solanum lycopersicum) have not been investigated. Here we identified four Swi3-like proteins from tomato, namely SlSWI3A, SlSWI3B, SlSWI3C, and SlSWI3D. Subcellular localization analysis revealed that all SlSWI3s are localized in the nucleus. The expression patterns showed that all SlSWI3s are ubiquitously expressed in all tissues and organs, and SlSWI3A and SlSWI3B can be induced by cold treatment. In addition, we found that SlSWI3B can form homodimers with itself and heterodimers with SlSWI3A and SlSWI3C. SlSWI3B can also interact with SlRIN and SlCHR8, two proteins involved in tomato reproductive development. Overexpression of SlSWI3C increased the leaf size in transgenic Arabidopsis with increased expression of GROWTH REGULATING FACTORs, such as GRF3, GRF5, and GRF6. Taken together, our results indicate that SlSWI3s may play important roles in tomato growth and development. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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14 pages, 3717 KiB  
Article
Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications
Int. J. Mol. Sci. 2019, 20(20), 5093; https://doi.org/10.3390/ijms20205093 - 14 Oct 2019
Cited by 13 | Viewed by 3183
Abstract
A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of [...] Read more.
A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of noncoding RNA molecules. Using a mass spectrometry-based proteomic approach, we examined the levels of acetylated histone peptide forms in Arabidopsis plants with a loss of function of histone deacetylase 6 (HDA6), and in plants germinated in the presence of HDA inhibitors trichostatin A (TSA) and sodium butyrate (NaB). Our analyses revealed particular lysine sites at histone sequences targeted by the HDA6 enzyme, and by TSA- and NaB-sensitive HDAs. Compared with plants exposed to drugs, more dramatic changes in the overall profiles of histone post-translational modifications were identified in hda6 mutants. However, loss of HDA6 was not sufficient by itself to induce hyperacetylation to the maximum degree, implying complementary activities of other HDAs. In contrast to hda6 mutants that did not exhibit any obvious phenotypic defects, the phenotypes of seedlings exposed to HDA inhibitors were markedly affected, showing that the effect of these drugs on early plant development is not limited to the modulation of histone acetylation levels. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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22 pages, 5431 KiB  
Article
Nuclear Disposition of Alien Chromosome Introgressions into Wheat and Rye Using 3D-FISH
Int. J. Mol. Sci. 2019, 20(17), 4143; https://doi.org/10.3390/ijms20174143 - 25 Aug 2019
Cited by 9 | Viewed by 3663
Abstract
During interphase, the chromosomes of eukaryotes decondense and they occupy distinct regions of the nucleus, called chromosome domains or chromosome territories (CTs). In plants, the Rabl’s configuration, with telomeres at one pole of nucleus and centromeres at the other, appears to be common, [...] Read more.
During interphase, the chromosomes of eukaryotes decondense and they occupy distinct regions of the nucleus, called chromosome domains or chromosome territories (CTs). In plants, the Rabl’s configuration, with telomeres at one pole of nucleus and centromeres at the other, appears to be common, at least in plants with large genomes. It is unclear whether individual chromosomes of plants adopt defined, genetically determined addresses within the nucleus, as is the case in mammals. In this study, the nuclear disposition of alien rye and barley chromosomes and chromosome arm introgressions into wheat while using 3D-FISH in various somatic tissues was analyzed. All of the introgressed chromosomes showed Rabl’s orientation, but their relative positions in the nuclei were less clear. While in most cases pairs of introgressed chromosomes occupied discrete positions, their association (proximity) along their entire lengths was rare, and partial association only marginally more frequent. This arrangement is relatively stable in various tissues and during various stages of the cell cycle. On the other hand, the length of a chromosome arm appears to play a role in its positioning in a nucleus: shorter chromosomes or chromosome arms tend to be located closer to the centre of the nucleus, while longer arms are more often positioned at the nuclear periphery. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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19 pages, 6841 KiB  
Article
Mutations in the Rice OsCHR4 Gene, Encoding a CHD3 Family Chromatin Remodeler, Induce Narrow and Rolled Leaves with Increased Cuticular Wax
Int. J. Mol. Sci. 2019, 20(10), 2567; https://doi.org/10.3390/ijms20102567 - 25 May 2019
Cited by 29 | Viewed by 5250
Abstract
Leaf blade width, curvature, and cuticular wax are important agronomic traits of rice. Here, we report the rice Oschr4-5 mutant characterized by pleiotropic phenotypes, including narrow and rolled leaves, enhanced cuticular wax deposition and reduced plant height and tiller number. The reduced leaf [...] Read more.
Leaf blade width, curvature, and cuticular wax are important agronomic traits of rice. Here, we report the rice Oschr4-5 mutant characterized by pleiotropic phenotypes, including narrow and rolled leaves, enhanced cuticular wax deposition and reduced plant height and tiller number. The reduced leaf width is caused by a reduced number of longitudinal veins and increased auxin content. The cuticular wax content was significantly higher in the Oschr4-5 mutant, resulting in reduced water loss rate and enhanced drought tolerance. Molecular characterization reveals that a single-base deletion results in a frame-shift mutation from the second chromodomain of OsCHR4, a CHD3 (chromodomain helicase DNA-binding) family chromatin remodeler, in the Oschr4-5 mutant. Expressions of seven wax biosynthesis genes (GL1-4, WSL4, OsCER7, LACS2, LACS7, ROC4 and BDG) and four auxin biosynthesis genes (YUC2, YUC3, YUC5 and YUC6) was up-regulated in the Oschr4-5 mutant. Chromatin immunoprecipitation assays revealed that the transcriptionally active histone modification H3K4me3 was increased, whereas the repressive H3K27me3 was reduced in the upregulated genes in the Oschr4-5 mutant. Therefore, OsCHR4 regulates leaf morphogenesis and cuticle wax formation by epigenetic modulation of auxin and wax biosynthetic genes expression. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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Review

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18 pages, 1154 KiB  
Review
Redox Components: Key Regulators of Epigenetic Modifications in Plants
Int. J. Mol. Sci. 2020, 21(4), 1419; https://doi.org/10.3390/ijms21041419 - 19 Feb 2020
Cited by 35 | Viewed by 5304
Abstract
Epigenetic modifications including DNA methylation, histone modifications, and chromatin remodeling are crucial regulators of chromatin architecture and gene expression in plants. Their dynamics are significantly influenced by oxidants, such as reactive oxygen species (ROS) and nitric oxide (NO), and antioxidants, like pyridine nucleotides [...] Read more.
Epigenetic modifications including DNA methylation, histone modifications, and chromatin remodeling are crucial regulators of chromatin architecture and gene expression in plants. Their dynamics are significantly influenced by oxidants, such as reactive oxygen species (ROS) and nitric oxide (NO), and antioxidants, like pyridine nucleotides and glutathione in plants. These redox intermediates regulate the activities and expression of many enzymes involved in DNA methylation, histone methylation and acetylation, and chromatin remodeling, consequently controlling plant growth and development, and responses to diverse environmental stresses. In recent years, much progress has been made in understanding the functional mechanisms of epigenetic modifications and the roles of redox mediators in controlling gene expression in plants. However, the integrated view of the mechanisms for redox regulation of the epigenetic marks is limited. In this review, we summarize recent advances on the roles and mechanisms of redox components in regulating multiple epigenetic modifications, with a focus of the functions of ROS, NO, and multiple antioxidants in plants. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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17 pages, 726 KiB  
Review
Roles of the INO80 and SWR1 Chromatin Remodeling Complexes in Plants
Int. J. Mol. Sci. 2019, 20(18), 4591; https://doi.org/10.3390/ijms20184591 - 17 Sep 2019
Cited by 23 | Viewed by 5370
Abstract
Eukaryotic genes are packed into a dynamic but stable nucleoprotein structure called chromatin. Chromatin-remodeling and modifying complexes generate a dynamic chromatin environment that ensures appropriate DNA processing and metabolism in various processes such as gene expression, as well as DNA replication, repair, and [...] Read more.
Eukaryotic genes are packed into a dynamic but stable nucleoprotein structure called chromatin. Chromatin-remodeling and modifying complexes generate a dynamic chromatin environment that ensures appropriate DNA processing and metabolism in various processes such as gene expression, as well as DNA replication, repair, and recombination. The INO80 and SWR1 chromatin remodeling complexes (INO80-c and SWR1-c) are ATP-dependent complexes that modulate the incorporation of the histone variant H2A.Z into nucleosomes, which is a critical step in eukaryotic gene regulation. Although SWR1-c has been identified in plants, plant INO80-c has not been successfully isolated and characterized. In this review, we will focus on the functions of the SWR1-c and putative INO80-c (SWR1/INO80-c) multi-subunits and multifunctional complexes in Arabidopsis thaliana. We will describe the subunit compositions of the SWR1/INO80-c and the recent findings from the standpoint of each subunit and discuss their involvement in regulating development and environmental responses in Arabidopsis. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology)
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