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      Chromatin-Based Epigenetic Regulation of Plant Abiotic Stress Response

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          Abstract

          Plants are continuously exposed to various abiotic and biotic factors limiting their growth and reproduction. In response, they need various sophisticated ways to adapt to adverse environmental conditions without compromising their proper development, reproductive success and eventually survival. This requires an intricate network to regulate gene expression at transcriptional and post-transcriptional levels, including epigenetic switches. Changes in chromatin modifications such as DNA and histone methylation have been observed in plants upon exposure to several abiotic stresses. In the present review, we highlight the changes of DNA methylation in diverse plants in response to several abiotic stresses such as salinity, drought, cold and heat. We also discuss the progresses made in understanding how these DNA methylation changes might contribute to the abiotic stress tolerance.

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          Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

          Shawn Cokus, Suhua Feng, Xiaoyu Zhang … (2008)
          Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.
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            Research on plant abiotic stress responses in the post-genome era: past, present and future.

            Takashi HIRAYAMA, Kazuo Shinozaki (2010)
            Understanding abiotic stress responses in plants is an important and challenging topic in plant research. Physiological and molecular biological analyses have allowed us to draw a picture of abiotic stress responses in various plants, and determination of the Arabidopsis genome sequence has had a great impact on this research field. The availability of the complete genome sequence has facilitated access to essential information for all genes, e.g. gene products and their function, transcript levels, putative cis-regulatory elements, and alternative splicing patterns. These data have been obtained from comprehensive transcriptome analyses and studies using full-length cDNA collections and T-DNA- or transposon-tagged mutant lines, which were also enhanced by genome sequence information. Moreover, studies on novel regulatory mechanisms involving use of small RNA molecules, chromatin modulation and genomic DNA modification have enabled us to recognize that plants have evolved complicated and sophisticated systems in response to complex abiotic stresses. Integrated data obtained with various 'omics' approaches have provided a more comprehensive picture of abiotic stress responses. In addition, research on stress responses in various plant species other than Arabidopsis has increased our knowledge regarding the mechanisms of plant stress tolerance in nature. Based on this progress, improvements in crop stress tolerance have been attempted by means of gene transfer and marker-assisted breeding. In this review, we summarize recent progress in abiotic stress studies, especially in the post-genomic era, and offer new perspectives on research directions for the next decade.
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              Epigenetic regulation of stress responses in plants.

              Viswanathan Chinnusamy, Jian-Kang Zhu (2009)
              Gene expression driven by developmental and stress cues often depends on nucleosome histone post-translational modifications and sometimes on DNA methylation. A number of studies have shown that these DNA and histone modifications play a key role in gene expression and plant development under stress. Most of these stress-induced modifications are reset to the basal level once the stress is relieved, while some of the modifications may be stable, that is, may be carried forward as 'stress memory' and may be inherited across mitotic or even meiotic cell divisions. Epigenetic stress memory may help plants more effectively cope with subsequent stresses. Comparative studies on stress-responsive epigenomes and transcriptomes will enhance our understanding of stress adaptation of plants.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Curr Genomics
                Journal ID (iso-abbrev): Curr. Genomics
                Journal ID (publisher-id): CG
                Title: Current Genomics
                Publisher: Bentham Science Publishers
                ISSN (Print): 1389-2029
                ISSN (Electronic): 1875-5488
                Publication date (Print): December 2016
                Publication date (Electronic): December 2016
                Volume: 17
                Issue: 6
                Pages: 490-498
                Affiliations
                [a ]National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
                Author notes
                [* ]Address correspondence to this author at the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India; Tel: 91-11-26735160; Fax: 91-11-26741658; 26741146;, E-mails: manoj_prasad@ 123456nipgr.ac.in , manoj_pds@ 123456yahoo.com
                [#]

                Equal contribution.

                Article
                Publisher ID: CG-17-490
                DOI: 10.2174/1389202917666160520103914
                PMC ID: 5282600
                PubMed ID: 28217005
                SO-VID: ad5b19ab-bade-49d8-ac3f-1b1375d06f74
                Copyright © ©2016 Bentham Science Publishers
                License:

                This is an open access article licensed under the terms of the Creative Commons Attribution-Non-Commercial 4.0 International Public License (CC BY-NC 4.0) (https://creativecommons.org/licenses/by-nc/4.0/legalcode), which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

                History
                Date received : 01 July 2015
                Date revision received : 10 December 2015
                Date accepted : 13 December 2015
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
                Keywords: abiotic stresses,dna methylation,epigenetic,histone methylation,plant adaption.
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: abiotic stresses, dna methylation, epigenetic, histone methylation, plant adaption.

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