**Contents**


#### **Anastassia Boudichevskaia, Andreas Houben, Anne Fiebig, Klara Prochazkova, Ales Pecinka and Inna Lermontova**

Depletion of *KNL2* Results in Altered Expression of Genes Involved in Regulation of the Cell Cycle, Transcription, and Development in *Arabidopsis* Reprinted from: *Int. J. Mol. Sci.* **2019**, *20*, 5726, doi:10.3390/ijms20225726 .............. **143**

#### **Saravana Kumar R. M., Yibin Wang, Xiaopan Zhang, Hui Cheng, Lirong Sun, Shibin He and Fushun Hao**

Redox Components: Key Regulators of Epigenetic Modifications in Plants Reprinted from: *Int. J. Mol. Sci.* **2020**, *21*, 1419, doi:10.3390/ijms21041419 .............. **162**

#### **About the Special Issue Editors**

**Jiˇr´ı Fajkus**: In 1987, he achieved MSc. and RNDr. titles from Biochemistry, J. E. Purkinje University Brno (now Masaryk University), Czech Republic. He was a research fellow and then a PhD student at the Institute of Biophysics, Czech Academy of Sciences. After completing his PhD in Biophysics in 1992 (thesis title 'Domains in the Eukaryotic Genomes'), he worked as a postdoctoral fellow at the Laval University Cancer Research Centre, Quebec, Canada (1992–1993, 1995, Lab. of Prof. Ronald Hancock). In 1996, he established his own research group at the Institute of Biophysics, Czech Academy of Sciences. In 1998, he also started a new research laboratory at the Faculty of Science, Masaryk University (MU), which now continues as the Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, MU. In 2003, he became an Associate Professor of Molecular Biology and Genetics, and in 2010, a Full Professor of Molecular Biology and Genetics, MU, Brno, Czech Republic. In 2011, he became the Head of the Mendel Centre for Plant Genomics and Proteomics at CEITEC—Central European Institute of Technology, MU. His research interests cover the biology of telomeres, chromatin structure and function, epigenetics, DNA repair and plant molecular biology. The major achievements of his research group include the first description of telomerase activity in plant cells (1996), stable telomere maintenance during plant ontogenesis and the reversible regulation of telomerase in plant cells (1998), the evolutionary variability of plant telomeres (2003), characterisation of a novel type of genome instability in plant CAF-1 mutants—specific and progressive loss of telomeres and rDNA, epigenetic reprogramming of rRNA genes (2010), characterization of AtTRB proteins as components of a plant shelterin-like telomere complex and epigenetic factor (2014, 2016), determination of unknown/non-canonical telomeres in plants of the genera Genlisea, Cestrum and Allium using the original BAL31-NGS method to identify telomere DNA, even in giant genomes with a small number of chromosomes for this purpose (2015–2017). The major recent achievement of his laboratory is the identification of the first bona fide telomerase RNA subunits across land plants with canonical and non-canonical telomeres, and the demonstration of their monophyletic origin (2019).

**Miloslava Fojtov´a**: In 1991, she achieved an MSc. title at Biochemistry, Charles University, Prague, Czech Republic. She was a research fellow and then a PhD student of Biophysics at the Institute of Biophysics, Czech Academy of Sciences. After completing her PhD in 2000 (thesis title 'Genetic and Epigenetic Changes of Plant Genomes'), she continued at the Institute of Biophysics, Department of Molecular Epigenetics as a postdoc. In 2010, she moved to Masaryk University, Brno, and joined Jirˇ´ı Fajkus' research group. In 2017, she became an Associate Professor of Biomolecular Chemistry, MU. Now, she works as a senior scientist and principal investigator at the Mendel Centre for Plant Genomics and Proteomics, CEITEC—Central European Institute of Technology, MU, and the Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, MU. Her research interests include plant telomeres and telomerase, epigenetic regulations and the impact of developmental and stress factors on plant genome and epigenome. She actively participates in the teaching and supervision of undergraduate and graduate students and significantly contributes to most research activities of J. Fajkus' research group.

#### *Editorial* **Chromatin, Epigenetics and Plant Physiology**

**Miloslava Fojtová 1,2,3 and Jiˇrí Fajkus 1,2,3,\***


Received: 7 April 2020; Accepted: 14 April 2020; Published: 16 April 2020

The ever-increasing interest in epigenetics comes from the fact that in the diverse life situations of organisms, e.g., in cell di fferentiation, developmental decisions, or responses to biotic and abiotic stresses, it is primarily the reprogramming of the regulation of the existing genetic information, rather than its direct change, that solves the problem. Epigenetic mechanisms allow the organism to channel the appropriate response through diverse particular molecular tools modifying distinct levels of the structure of chromatin. Chromatin is thus marked with certain signals, for example, DNA methylation, posttranslational modifications of histones, incorporation of specific histone variants, or chromatin remodeling. These signals, written by respective enzymes and complexes, termed as epigenetic writers (e.g., DNA methyltransferases, histone methyltransferases, and histone acetyltransferases) have to find their readers—biomolecules recognizing the specific mark, and erasers which are capable of resetting the program. Recent data sugges<sup>t</sup> a deep interconnection of individual epigenetic players, which frequently act together as components of the same multi-subunit complexes. For example, methylcytosine binding protein MeCP2 (a reader) recruits histone deacetylase (an eraser) and H3K9 histone methyltransferase Suv39h1 (a writer), and in this way reinforces the repressive state of a chromatin region [1,2]. Recent research in plants brings many novel findings elucidating the interdependence of diverse epigenetic mechanisms and their crosstalk with various signaling pathways, including the action of phytohormones and reactive oxygen and nitrogen species. Using these molecular tools, chromatin structure decides which particular set of genes will be active in a particular physiological process.

The special issue "Chromatin, Epigenetics and Plant Physiology" in the International Journal of Molecular Sciences comprises two review articles and eight original research papers (Table 1). All contributions deal with important aspects of epigenetic regulations of crucial cellular processes involved in plant growth and development.

Four articles, one review, and three research papers deal with chromatin remodeling complexes. Wang et al. [3] provide a review on the role of Arabidopsis SWR1 and INO80 chromatin remodeling complexes involved in the regulation of the replacement of nucleosomal H2A/H2B dimers with H2A.Z/H2B. The authors describe the composition of the SWR1/INO80-c complex and discuss its diverse nuclear roles ranging from repair processes to regulation of gene expression. Guo et al. [4] report on the involvement of the chromatin remodeler encoded by the *OsCHR4* gene in regulation of rice leaf morphology, via modulation of accumulation of cuticle wax on leaf surfaces and auxin biosynthesis. Expression profiles and subcellular localizations of tomato SWI3-like proteins were studied by Zhao et al. [5]. The authors further identify interactions of these subunits of the chromatin remodeling complex with proteins participating in the reproductive development. Their observations support the idea of evolutionary conservation of SWI3 physiological functions in di fferent plant species. Similarly, the involvement of the SWI subunits of the chromatin remodeling complex in temperature-dependent regulation of plant growth and developmental responses in Arabidopsis is reported by Gratkowska-Zmuda et al. [6]. Altogether, these results demonstrate the importance of the proper chromatin remodeling in crucial cellular processes, including gene expression, cell cycle regulation, DNA replication and repair, and hormone signaling.


**Table 1.** Contributors to the special issue "Chromatin, Epigenetics and Plant Physiology".

Results presented in two papers within the special issue "Chromatin, Epigenetics, and Plant Physiology" were obtained using specific advanced methodical approaches. Circular chromosome conformation capture (4C)-based method was utilized by Krispil et al. [7] for the detection of the entire scope of T-DNA insertions, by capturing the local enrichment of spatial chromosomal associations in their genomic proximity without prior knowledge of their genomic locations in Arabidopsis transgenic lines. This approach enables the identification of previously unmapped T-DNA insertions and related chromosomal rearrangements and is applicable to any plant with a sequenced genome. Lochmanová et al. [8] studied the acetylation of histone proteins by a mass spectrometry-based proteomic approach. They conclude that the effect of epigenetically active drugs on early plant development is complex and is not restricted to the ability of these compounds to modulate the levels of histone acetylation marks.

Koláckov ˇ á et al. [9] solved an interesting problem of the spatial organization of parental genomes in the somatic nuclei of interspecific plant hybrids. They demonstrate that domains of introgressed chromosomes are highly stable among the tissue types and during the cell cycle phases. High-throughput sequencing of Arabidopsis seedlings exposed to methyl jasmonic acid was performed by Zhang et al. [10] to identify differentially expressed circular RNAs. Based on their data, differentially expressed circular RNAs are involved in metabolic and developmental processes and are supposed to play important roles in methyl jasmonic acid-mediated signaling. Boudichevskaia et al. [11] dealt with the characterization of the role of Arabidopsis KNL2 (kinetochore null 2), which is important for deposition of CENH3 at centromeric regions. Transcriptomic analysis of mutant plants reveals that the *KNL2* gene loss of function affects processes of cell cycle regulation, transcription, development, and DNA repair. In the review article by R.M.S. et al. [12], the impact of redox components on activities of important epigenetic regulators was described. Authors provide an integrated view on the roles

of oxidants (reactive oxygen species and nitric oxide) and antioxidants (pyridine nucleotides and glutathione) in the modulation of DNA methylation and histone modifications in plants.

Together, this collection offers diverse insights into the current plant epigenetics to allow readers to update their knowledge on the described phenomena and mechanisms in this highly complex and quickly evolving field.

**Funding:** M.F. and J.F. are supported by the European Regional Development Fund-Project 'SINGING PLANT' (CZ.02.1.01/0.0/0.0/16\_026/0008446) and the Ministry of Education, Youth and Sports of the Czech Republic—project CEITEC 2020 (LQ1601).

**Conflicts of Interest:** The authors declare no conflict of interest.
