Chromatin Integration and Dynamics of Environmental Cues

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 15899

Special Issue Editors


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Guest Editor
Department of Biosciences, University of Milan, 20133 Milan, Italy
Interests: epigenetics; abiotic stress; light signaling; Arabidopsis and bio-refinery crops
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Guest Editor
CRAG (Centre for Research in Agricultural Genomics), 08193 Cerdanyola del Vallès (Barcelona), Spain
Interests: epigenetics; histone modifications; light signalling; shade response; seed development; Arabidopsis

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Guest Editor
Department of Agronomy Animal Food Natural Resources and Environment (DAFNAE), University of Padova, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
Interests: epigenetics of crop adaptation to environmental challenges
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Guest Editor
Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
Interests: gene regulation; nuclear organization; cell biology

Special Issue Information

Dear Colleagues,

Chromatin represents the nuclear complex formed between DNA, RNA and proteins contained in eukaryotic cells. Chromatin structure and function are highly dynamic and responsive to environmental cues. Such responses are especially reflected in the plasticity of plants, sessile organisms that learn to adapt and alter their development and growth according to their surroundings. In this context, the ability of the epigenetic status to rapidly respond and modify gene expression is a key component of plants’ flexibility and power to survive in a constantly changing environment.

This Special Issue is open to research and review articles presenting novel findings focusing on the dynamics and stability of chromatin states and modifications and their integration in regulating environmental responses, including drought, temperature and light.

In particular, we welcome research paper on the following topics:

  • Histone modifiers and abiotic/biotic stress;
  • Genome adaptation and stability;
  • Epigenetic integration of signaling responses;
  • RNA structure.

Dr. Giorgio Perrella
Dr. Jordi Moreno-Romero
Dr. Serena Varotto
Dr. Stefanie Rosa
Guest Editors

Manuscript Submission Information

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Keywords

  • response/adaptation to environmental changes
  • plant epigenetics
  • drought
  • temperature
  • nuclear architecture
  • chromatin organization
  • chromatin regulation
  • stress memory
  • histone modifications
  • priming
  • transcriptional reprogramming
  • gene expression
  • non-coding RNAs

Published Papers (4 papers)

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Research

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31 pages, 4986 KiB  
Article
DNA Methylation Changes and Its Associated Genes in Mulberry (Morus alba L.) Yu-711 Response to Drought Stress Using MethylRAD Sequencing
by Michael Ackah, Liangliang Guo, Shaocong Li, Xin Jin, Charles Asakiya, Evans Tawiah Aboagye, Feng Yuan, Mengmeng Wu, Lionnelle Gyllye Essoh, Daniel Adjibolosoo, Thomas Attaribo, Qiaonan Zhang, Changyu Qiu, Qiang Lin and Weiguo Zhao
Plants 2022, 11(2), 190; https://doi.org/10.3390/plants11020190 - 12 Jan 2022
Cited by 15 | Viewed by 2994
Abstract
Drought stress remains one of the most detrimental environmental cues affecting plant growth and survival. In this work, the DNA methylome changes in mulberry leaves under drought stress (EG) and control (CK) and their impact on gene regulation were investigated by MethylRAD sequencing. [...] Read more.
Drought stress remains one of the most detrimental environmental cues affecting plant growth and survival. In this work, the DNA methylome changes in mulberry leaves under drought stress (EG) and control (CK) and their impact on gene regulation were investigated by MethylRAD sequencing. The results show 138,464 (37.37%) and 56,241 (28.81%) methylation at the CG and CWG sites (W = A or T), respectively, in the mulberry genome between drought stress and control. The distribution of the methylome was prevalent in the intergenic, exonic, intronic and downstream regions of the mulberry plant genome. In addition, we discovered 170 DMGs (129 in CG sites and 41 in CWG sites) and 581 DMS (413 in CG sites and 168 in CWG sites). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicates that phenylpropanoid biosynthesis, spliceosome, amino acid biosynthesis, carbon metabolism, RNA transport, plant hormone, signal transduction pathways, and quorum sensing play a crucial role in mulberry response to drought stress. Furthermore, the qRT-PCR analysis indicates that the selected 23 genes enriched in the KEGG pathways are differentially expressed, and 86.96% of the genes share downregulated methylation and 13.04% share upregulation methylation status, indicating the complex link between DNA methylation and gene regulation. This study serves as fundamentals in discovering the epigenomic status and the pathways that will significantly enhance mulberry breeding for adaptation to a wide range of environments. Full article
(This article belongs to the Special Issue Chromatin Integration and Dynamics of Environmental Cues)
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13 pages, 1592 KiB  
Article
The Role of DNA Topoisomerase Binding Protein 1 (TopBP1) in Genome Stability in Arabidopsis
by Pablo Parra-Nunez, Claire Cooper and Eugenio Sanchez-Moran
Plants 2021, 10(12), 2568; https://doi.org/10.3390/plants10122568 - 24 Nov 2021
Cited by 4 | Viewed by 2238
Abstract
DNA topoisomerase II (TOPII) plays a very important role in DNA topology and in different biological processes such as DNA replication, transcription, repair, and chromosome condensation in higher eukaryotes. TOPII has been found to interact directly with a protein called topoisomerase II binding [...] Read more.
DNA topoisomerase II (TOPII) plays a very important role in DNA topology and in different biological processes such as DNA replication, transcription, repair, and chromosome condensation in higher eukaryotes. TOPII has been found to interact directly with a protein called topoisomerase II binding protein 1 (TopBP1) which also seems to have important roles in DNA replication and repair. In this study, we conducted different experiments to assess the roles of TopBP1 in DNA repair, mitosis, and meiosis, exploring the relationship between TOPII activity and TopBP1. We found that topbp1 mutant seedlings of Arabidopsis thaliana were hypersensitive to cisplatin treatment and the inhibition of TOPII with etoposide produced similar hypersensitivity levels. Furthermore, we recognised that there were no significant differences between the WT and topbp1 seedlings treated with cisplatin and etoposide together, suggesting that the hypersensitivity to cisplatin in the topbp1 mutant could be related to the functional interaction between TOPII and TopBP1. Somatic and meiotic anaphase bridges appeared in the topbp1 mutant at similar frequencies to those when TOPII was inhibited with merbarone, etoposide, or ICFR-187. The effects on meiosis of TOPII inhibition were produced at S phase/G2 stage, suggesting that catenanes could be produced at the onset of meiosis. Thus, if the processing of the catenanes is impaired, some anaphase bridges can be formed. Also, the appearance of anaphase bridges at first and second division is discussed. Full article
(This article belongs to the Special Issue Chromatin Integration and Dynamics of Environmental Cues)
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Review

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10 pages, 989 KiB  
Review
The Epigenetic Mechanisms Underlying Thermomorphogenesis and Heat Stress Responses in Arabidopsis
by Anna Zioutopoulou, Eirini Patitaki, Tianyuan Xu and Eirini Kaiserli
Plants 2021, 10(11), 2439; https://doi.org/10.3390/plants10112439 - 12 Nov 2021
Cited by 7 | Viewed by 3592
Abstract
Integration of temperature cues is crucial for plant survival and adaptation. Global warming is a prevalent issue, especially in modern agriculture, since the global rise in average temperature is expected to impact crop productivity worldwide. Hence, better understanding of the mechanisms by which [...] Read more.
Integration of temperature cues is crucial for plant survival and adaptation. Global warming is a prevalent issue, especially in modern agriculture, since the global rise in average temperature is expected to impact crop productivity worldwide. Hence, better understanding of the mechanisms by which plants respond to warmer temperatures is very important. This review focuses on the epigenetic mechanisms implicated in plant responses to high temperature and distinguishes the different epigenetic events that occur at warmer average temperatures, leading to thermomorphogenic responses, or subjected to extreme warm temperatures, leading to heat stress. Full article
(This article belongs to the Special Issue Chromatin Integration and Dynamics of Environmental Cues)
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21 pages, 2701 KiB  
Review
Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues
by Qingwen Shen, Yisheng Lin, Yingbo Li and Guifeng Wang
Plants 2021, 10(6), 1165; https://doi.org/10.3390/plants10061165 - 08 Jun 2021
Cited by 18 | Viewed by 6012
Abstract
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and [...] Read more.
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses. Full article
(This article belongs to the Special Issue Chromatin Integration and Dynamics of Environmental Cues)
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