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Chromatin, Epigenetics and Plant Physiology 2.0

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

Deadline for manuscript submissions: closed (25 February 2023) | Viewed by 5930

Special Issue Editors


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Guest Editor
Mendel Centre for Plant Genomics and Proteomics, Masaryk University, Brno, Czech Republic
Interests: telomeres; telomerase; chromatin; epigenetics; genome stability; DNA repair; plant molecular biology
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E-Mail Website
Guest Editor
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 (SI) of IJMS on “Chromatin, Epigenetics and Plant Physiology”. This SI will focus on current progress in understanding the role of the 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, require understanding the structure and function of chromatin, and its specific domains, such as 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 in sessile organisms, display an enormous capacity to cope with environmental stress. In these processes, epigenetic mechanisms show crosstalk with plant signaling pathways mediated by phytohormones. Current advances in methodological tools have made it possible to investigate the chromatin structure, starting from its basic level, the nucleosome, up to the higher-order structures (chromatin fibers, 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
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

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Published Papers (2 papers)

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Research

16 pages, 2679 KiB  
Article
Unravelling Differential DNA Methylation Patterns in Genotype Dependent Manner under Salinity Stress Response in Chickpea
by Khushboo Gupta and Rohini Garg
Int. J. Mol. Sci. 2023, 24(3), 1863; https://doi.org/10.3390/ijms24031863 - 18 Jan 2023
Cited by 4 | Viewed by 2409
Abstract
DNA methylation is one of the epigenetic mechanisms that govern gene regulation in response to abiotic stress in plants. Here, we analyzed the role of epigenetic variations by exploring global DNA methylation and integrating it with differential gene expression in response to salinity [...] Read more.
DNA methylation is one of the epigenetic mechanisms that govern gene regulation in response to abiotic stress in plants. Here, we analyzed the role of epigenetic variations by exploring global DNA methylation and integrating it with differential gene expression in response to salinity stress in tolerant and sensitive chickpea genotypes. Genome-wide DNA methylation profiles showed higher CG methylation in the gene body regions and higher CHH methylation in the TE body regions. The analysis of differentially methylated regions (DMRs) suggested more hyper-methylation in response to stress in the tolerant genotype compared to the sensitive genotype. We observed higher enrichment of CG DMRs in genes and CHH DMRs in transposable elements (TEs). A positive correlation of gene expression with CG gene body methylation was observed. The enrichment analysis of DMR-associated differentially expressed genes revealed they are involved in biological processes, such as lateral root development, transmembrane transporter activity, GTPase activity, and regulation of gene expression. Further, a high correlation of CG methylation with CHG and CHH methylation under salinity stress was revealed, suggesting crosstalk among the methylation contexts. Further, we observed small RNA-mediated CHH hypermethylation in TEs. Overall, the interplay between DNA methylation, small RNAs, and gene expression provides new insights into the regulatory mechanism underlying salinity stress response in chickpeas. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology 2.0)
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21 pages, 4725 KiB  
Article
The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum
by Axel Poulet, Ellyn Rousselot, Stéphane Téletchéa, Céline Noirot, Yannick Jacob, Josien van Wolfswinkel, Christophe Thiriet and Céline Duc
Int. J. Mol. Sci. 2023, 24(2), 1051; https://doi.org/10.3390/ijms24021051 - 5 Jan 2023
Viewed by 2830
Abstract
The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. Physarum polycephalum [...] Read more.
The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. Physarum polycephalum is a Mycetozoan, a clade located at the crown of the eukaryotic tree. We previously found that histones, which are highly conserved between plants and animals, are also highly conserved in Physarum. However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in Physarum and their evolution relative to animal and plants. Most of the known histone chaperones and their functional domains are conserved as well as key residues required for histone and chaperone interactions. Physarum is divergent from yeast, plants and animals, but PpHIRA, PpCABIN1 and PpSPT6 are similar in structure to plant orthologues. PpFACT is closely related to the yeast complex, and the Physarum genome encodes the animal-specific APFL chaperone. Furthermore, we performed RNA sequencing to monitor chaperone expression during the cell cycle and uncovered two distinct patterns during S-phase. In summary, our study demonstrates the conserved role of histone chaperones in handling histones in an early-branching eukaryote. Full article
(This article belongs to the Special Issue Chromatin, Epigenetics and Plant Physiology 2.0)
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