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      Use of MSAP Markers to Analyse the Effects of Salt Stress on DNA Methylation in Rapeseed ( Brassica napus var. oleifera)

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          Abstract

          Excessive soil salinity is a major ecological and agronomical problem, the adverse effects of which are becoming a serious issue in regions where saline water is used for irrigation. Plants can employ regulatory strategies, such as DNA methylation, to enable relatively rapid adaptation to new conditions. In this regard, cytosine methylation might play an integral role in the regulation of gene expression at both the transcriptional and post-transcriptional levels. Rapeseed, which is the most important oilseed crop in Europe, is classified as being tolerant of salinity, although cultivars can vary substantially in their levels of tolerance. In this study, the Methylation Sensitive Amplified Polymorphism (MSAP) approach was used to assess the extent of cytosine methylation under salinity stress in salinity-tolerant (Exagone) and salinity-sensitive (Toccata) rapeseed cultivars. Our data show that salinity affected the level of DNA methylation. In particular methylation decreased in Exagone and increased in Toccata. Nineteen DNA fragments showing polymorphisms related to differences in methylation were sequenced. In particular, two of these were highly similar to genes involved in stress responses (Lacerata and trehalose-6-phosphatase synthase S4) and were chosen to further characterization. Bisulfite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied. In particular, our data show that salinity stress influences the expression of the two stress-related genes. Moreover, we quantified the level of trehalose in Exagone shoots and found that it was correlated to TPS4 expression and, therefore, to DNA methylation. In conclusion, we found that salinity could induce genome-wide changes in DNA methylation status, and that these changes, when averaged across different genotypes and developmental stages, accounted for 16.8% of the total site-specific methylation differences in the rapeseed genome, as detected by MSAP analysis.

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          Most cited references34

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

          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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            Salt tolerance and salinity effects on plants: a review.

            Plants exposed to salt stress undergo changes in their environment. The ability of plants to tolerate salt is determined by multiple biochemical pathways that facilitate retention and/or acquisition of water, protect chloroplast functions, and maintain ion homeostasis. Essential pathways include those that lead to synthesis of osmotically active metabolites, specific proteins, and certain free radical scavenging enzymes that control ion and water flux and support scavenging of oxygen radicals or chaperones. The ability of plants to detoxify radicals under conditions of salt stress is probably the most critical requirement. Many salt-tolerant species accumulate methylated metabolites, which play crucial dual roles as osmoprotectants and as radical scavengers. Their synthesis is correlated with stress-induced enhancement of photorespiration. In this paper, plant responses to salinity stress are reviewed with emphasis on physiological, biochemical, and molecular mechanisms of salt tolerance. This review may help in interdisciplinary studies to assess the ecological significance of salt stress.
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              The DNA methyltransferases of mammals.

              T Bestor (2000)
              The biological significance of 5-methylcytosine was in doubt for many years, but is no longer. Through targeted mutagenesis in mice it has been learnt that every protein shown by biochemical tests to be involved in the establishment, maintenance or interpretation of genomic methylation patterns is encoded by an essential gene. A human genetic disorder (ICF syndrome) has recently been shown to be caused by mutations in the DNA methyltransferase 3B (DNMT3B) gene. A second human disorder (Rett syndrome) has been found to result from mutations in the MECP2 gene, which encodes a protein that binds to methylated DNA. Global genome demethylation caused by targeted mutations in the DNA methyltransferase-1 (Dnmt1) gene has shown that cytosine methylation plays essential roles in X-inactivation, genomic imprinting and genome stabilization. The majority of genomic 5-methylcytosine is now known to enforce the transcriptional silence of the enormous burden of transposons and retroviruses that have accumulated in the mammalian genome. It has also become clear that programmed changes in methylation patterns are less important in the regulation of mammalian development than was previously believed. Although a number of outstanding questions have yet to be answered (one of these questions involves the nature of the cues that designate sites for methylation at particular stages of gametogenesis and early development), studies of DNA methyltransferases are likely to provide further insights into the biological functions of genomic methylation patterns.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2013
                23 September 2013
                : 8
                : 9
                : e75597
                Affiliations
                [1 ]Department of Applied Biology, University of Perugia, Perugia, Italy
                [2 ]Department of Agricultural and Environmental Science, University of Perugia, Perugia, Italy
                [3 ]Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Naples, Italy
                [4 ]Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
                Cankiri Karatekin University, Turkey
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: GM RP PB EA. Performed the experiments: GM RP LR SL EA. Analyzed the data: GM AT MC EA. Contributed reagents/materials/analysis tools: SL MG MF SL EA. Wrote the manuscript: GM LR SL EA. Revised the manuscript: GM EA.

                Article
                PONE-D-13-05523
                10.1371/journal.pone.0075597
                3781078
                24086583
                3a50d796-ccdb-452d-b7bc-9b986055f0da
                Copyright @ 2013

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 7 February 2013
                : 18 August 2013
                Funding
                This study was supported by the University of Perugia - Department of Applied Biology projects - Molecular characterization of agronomically important species (project code ALBERPREST) Associazione Produttori Olivicoli (A.PR.OL) ( http://www.aprolperugia.it/aprol/index.php) Molecular characterization of oil crops (project code APRO09ALB and APRO10ALB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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