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19 pages, 3530 KiB

Open AccessArticle

Dynamics of the Methylome and Transcriptome during the Regeneration of Rice

by Fei-Man Hsu, Moloya Gohain, Archana Allishe, Yan-Jiun Huang, Jo-Ling Liao, Lin-Yun Kuang and Pao-Yang Chen

Epigenomes 2018, 2(3), 14; https://doi.org/10.3390/epigenomes2030014 - 21 Jul 2018

Cited by 16 | Viewed by 7422

Abstract

Oryza sativa indica (cv. IR64) and Oryza sativa japonica (cv. TNG67) vary in their regeneration efficiency. Such variation may occur in response to cultural environments that induce somaclonal variation. Somaclonal variations may arise from epigenetic factors, such as DNA methylation. We [...] Read more.

Oryza sativa indica (cv. IR64) and Oryza sativa japonica (cv. TNG67) vary in their regeneration efficiency. Such variation may occur in response to cultural environments that induce somaclonal variation. Somaclonal variations may arise from epigenetic factors, such as DNA methylation. We hypothesized that somaclonal variation may be associated with the differential regeneration efficiency between IR64 and TNG67 through changes in DNA methylation. We generated the stage-associated methylome and transcriptome profiles of the embryo, induced calli, sub-cultured calli, and regenerated calli (including both successful and failed regeneration) of IR64 and TNG67. We found that stage-associated changes are evident by the increase in the cytosine methylation of all contexts upon induction and decline upon regeneration. These changes in the methylome are largely random, but a few regions are consistently targeted at the later stages of culture. The expression profiles showed a dominant tissue-specific difference between the embryo and the calli. A prominent cultivar-associated divide in the global methylation pattern was observed, and a subset of cultivar-associated differentially methylated regions also showed stage-associated changes, implying a close association between differential methylation and the regeneration programs of these two rice cultivars. Based on these findings, we speculate that the differential epigenetic regulation of stress response and developmental pathways may be coupled with genetic differences, ultimately leading to differential regeneration efficiency. The present study elucidates the impact of tissue culture on callus formation and delineates the impact of stage and cultivar to determine the dynamics of the methylome and transcriptome in culture. Full article

(This article belongs to the Special Issue Plant Epigenome Dynamics)

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27 pages, 3908 KiB

Open AccessArticle

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

by Moumouni Konate, Michael J. Wilkinson, Benjamin T. Mayne, Stephen M. Pederson, Eileen S. Scott, Bettina Berger and Carlos M. Rodriguez Lopez

Epigenomes 2018, 2(2), 12; https://doi.org/10.3390/epigenomes2020012 - 20 Jun 2018

Cited by 22 | Viewed by 9521

Abstract

Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated with the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response [...] Read more.

Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated with the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response to salt stress has been relatively poorly studied among crops such as barley. Here, we assessed the extent of salt-induced alterations of DNA methylation in barley and their putative role in perturbed gene expression. Using Next Generation Sequencing, we screened the leaf and root methylomes of five divergent barley varieties grown under control and three salt concentrations, to seek genotype independent salt-induced changes in DNA methylation. Salt stress caused increased methylation in leaves but diminished methylation in roots with a higher number of changes in leaves than in roots, indicating that salt induced changes to global methylation are organ specific. Differentially Methylated Markers (DMMs) were mostly located in close proximity to repeat elements, but also in 1094 genes, of which many possessed gene ontology (GO) terms associated with plant responses to stress. Identified markers have potential value as sentinels of salt stress and provide a starting point to allow understanding of the functional role of DNA methylation in facilitating barley’s response to this stressor. Full article

(This article belongs to the Special Issue Plant Epigenome Dynamics)

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1621 KiB

Open AccessArticle

Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

by Conchita Alonso, Mónica Medrano, Ricardo Pérez, Pilar Bazaga and Carlos M. Herrera

Epigenomes 2017, 1(3), 16; https://doi.org/10.3390/epigenomes1030016 - 2 Nov 2017

Cited by 13 | Viewed by 5916

Abstract

Experimental alteration of DNA methylation is a suitable tool to infer the relationship between phenotypic and epigenetic variation in plants. A detailed analysis of the genome-wide effect of demethylating agents, such as 5-azacytidine (5azaC), and zebularine is only available for the model species [...] Read more.

Experimental alteration of DNA methylation is a suitable tool to infer the relationship between phenotypic and epigenetic variation in plants. A detailed analysis of the genome-wide effect of demethylating agents, such as 5-azacytidine (5azaC), and zebularine is only available for the model species Arabidopsis thaliana, which suggests that 5azaC may have a slightly larger effect. In this study, global methylation estimates obtained by high-performance liquid chromatography (HPLC) analyses were conducted to investigate the impact of 5azaC treatment on leaf and root tissue in Erodium cicutarium (Geraniaceae), which is an annual herb native to Mediterranean Europe that is currently naturalized in all continents, sometimes becoming invasive. We used seeds collected from two natural populations in SE Spain. Root tissue of the second generation (F2) greenhouse-grown seedlings had a significantly lower global cytosine methylation content than leaf tissue (13.0 vs. 17.7% of all cytosines). Leaf tissue consistently decreased methylation after treatment, but the response of root tissue varied according to seed provenance, suggesting that genetic background can mediate the response to experimental demethylation. We also found that both leaf number and leaf length were reduced in treated seedlings supporting a consistent phenotypic effect of the treatment regardless of seedling provenance. These findings suggest that, although the consequences of experimental demethylation may be tissue- and background-specific, this method is effective in altering early seedling development, and can thus be useful in ecological epigenetic studies that are aiming to investigate the links between epigenetic and phenotypic variation in non-model plant species. Full article

(This article belongs to the Special Issue Plant Epigenome Dynamics)

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6519 KiB

Open AccessArticle

Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana

by Julia Engelhorn, Robert Blanvillain, Christian Kröner, Hugues Parrinello, Marine Rohmer, David Posé, Felix Ott, Markus Schmid and Cristel C. Carles

Epigenomes 2017, 1(2), 8; https://doi.org/10.3390/epigenomes1020008 - 29 Jun 2017

Cited by 29 | Viewed by 13258

Abstract

Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine [...] Read more.

Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics. Full article

(This article belongs to the Special Issue Plant Epigenome Dynamics)

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1519 KiB

Open AccessArticle

Increase of DNA Methylation at the HvCKX2.1 Promoter by Terminal Drought Stress in Barley

by Korana Surdonja, Kai Eggert, Mohammad-Reza Hajirezaei, Vokkaliga Thammegowda Harshavardhan, Christiane Seiler, Nicolaus Von Wirén, Nese Sreenivasulu and Markus Kuhlmann

Epigenomes 2017, 1(2), 9; https://doi.org/10.3390/epigenomes1020009 - 27 Jun 2017

Cited by 39 | Viewed by 7674

Abstract

Terminal drought stress during grain filling is the major abiotic factor that limits crop yield in barley. The mother plant acclimates to the environment and perceives signals that result in a change of the physiological state within the grain and therefore affect the [...] Read more.

Terminal drought stress during grain filling is the major abiotic factor that limits crop yield in barley. The mother plant acclimates to the environment and perceives signals that result in a change of the physiological state within the grain and therefore affect the seed development and germination of the next generation. Small regulatory RNAs have been described to be involved in plant drought stress response by suppressing the respective target genes. Based on their origin and function, these small RNAs are classified as micro RNAs (miRNA), short interfering RNAs (siRNA) or heterochromatic small interfering RNA (hc-siRNA). In addition, 24mer sized hc-siRNAs are associated with RNA directed DNA methylation (RdDM) and transcriptional gene silencing (TGS). The analysis of hc-siRNA by small RNA sequencing in barley caryopses after imposition of terminal drought stress allowed the identification of stress specific 24mers. Based on the sequence homology of the siRNAs to the promoter region of CYTOKININ-OXIDASE 2.1 (HvCKX2.1), this putative target gene was selected for further investigation. Terminal drought stress leads to an increased level of DNA methylation at the HvCKX2.1 promoter and the seeds derived from drought stressed plants showed faster shoot emergence. Accumulation of cytokinin ribosides, which are the known substrates of cytokinin-oxidase, can explain the observed phenotype of faster shoot emergence from seeds of drought stressed mother plants. Analysis of transgenic plants with modulated levels of abscisic acid (ABA) in the grain confirmed the ABA/drought stress responsive ProHvCKX2.1 methylation and correlation with shoot emergence speed. Full article

(This article belongs to the Special Issue Plant Epigenome Dynamics)

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7489 KiB

Open AccessArticle

Epigenetic Regulation of a Heat-Activated Retrotransposon in Cruciferous Vegetables

by Kosuke Nozawa, Yuki Kawagishi, Akira Kawabe, Mio Sato, Yukari Masuta, Atsushi Kato and Hidetaka Ito

Epigenomes 2017, 1(1), 7; https://doi.org/10.3390/epigenomes1010007 - 7 Jun 2017

Cited by 5 | Viewed by 5508

Abstract

Transposable elements (TEs) are highly abundant in plant genomes. Environmental stress is one of the critical stimuli that activate TEs. We analyzed a heat-activated retrotransposon, named ONSEN, in cruciferous vegetables. Multiple copies of ONSEN-like elements (OLEs) were found in all of the cruciferous [...] Read more.

Transposable elements (TEs) are highly abundant in plant genomes. Environmental stress is one of the critical stimuli that activate TEs. We analyzed a heat-activated retrotransposon, named ONSEN, in cruciferous vegetables. Multiple copies of ONSEN-like elements (OLEs) were found in all of the cruciferous vegetables that were analyzed. The copy number of OLE was high in Brassica oleracea, which includes cabbage, cauliflower, broccoli, Brussels sprout, and kale. Phylogenic analysis demonstrated that some OLEs transposed after the allopolyploidization of parental Brassica species. Furthermore, we found that the high copy number of OLEs in B. oleracea appeared to induce transpositional silencing through epigenetic regulation, including DNA methylation. The results of this study would be relevant to the understanding of evolutionary adaptations to thermal environmental stress in different species. Full article

(This article belongs to the Special Issue Plant Epigenome Dynamics)

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1668 KiB

Open AccessArticle

The Pea (Pisum sativum L.) Rogue Paramutation is Accompanied by Alterations in the Methylation Pattern of Specific Genomic Sequences

by Tatiana E. Santo, Ricardo J. Pereira and José M. Leitão

Epigenomes 2017, 1(1), 6; https://doi.org/10.3390/epigenomes1010006 - 18 May 2017

Cited by 8 | Viewed by 7505

Abstract

The spontaneous emergence among common pea (Pisum sativum L.) cultivars of off-type rogue plants exhibiting leaves with narrower and pointed leaflets and stipules and the non-Mendelian inheritance of this new phenotype were first described in the early 20th century. However, so far, [...] Read more.

The spontaneous emergence among common pea (Pisum sativum L.) cultivars of off-type rogue plants exhibiting leaves with narrower and pointed leaflets and stipules and the non-Mendelian inheritance of this new phenotype were first described in the early 20th century. However, so far, no studies at the molecular level of this first identified case of paramutation have been carried out. In this study, we show for the first time that the pea rogue paramutation is accompanied by alterations in the methylation status of specific genomic sequences. Although, no significant differences were observed in the genome-wide DNA methylation in leaves of non-rogue cv. Onward in comparison to its rogue paramutant line JI2723, 22 DNA sequences were identified by methylation-sensitive amplified fragment length polymorphisms (MS-AFLP) analysis as differentially methylated in the two epigenomes. Mitotically inherited through all leaf tissues, the differential methylation patterns were also found to be meiotically inherited and conserved in pollen grains for 12 out of the 22 sequences. Fourteen of the sequences were successfully amplified in cDNA but none of them exhibited significant differential expression in the two contrasting epigenotypes. The further exploitation of the present research results on the way towards the elucidation of the molecular mechanisms behind this interesting epigenetic phenomenon is discussed. Full article

(This article belongs to the Special Issue Plant Epigenome Dynamics)

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Review

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527 KiB

Open AccessReview

DNA Methylation in Rice and Relevance for Breeding

by Sophie Lanciano and Marie Mirouze

Epigenomes 2017, 1(2), 10; https://doi.org/10.3390/epigenomes1020010 - 4 Jul 2017

Cited by 15 | Viewed by 8183

Abstract

The challenge of sustaining food security in the context of global changes is at the heart of plant research. Environmental stresses, in particular, are known to impact genome stability and epigenetic mechanisms. Epigenetic pathways are well characterized in plants, particularly in the dicotyledon [...] Read more.

The challenge of sustaining food security in the context of global changes is at the heart of plant research. Environmental stresses, in particular, are known to impact genome stability and epigenetic mechanisms. Epigenetic pathways are well characterized in plants, particularly in the dicotyledon model plant Arabidopsis thaliana, but an increasing number of epigenetic and epigenomic studies are also performed on rice (Oryza sativa). Rice represents a major food crop of worldwide importance and is also a good model for monocotyledons owing to its relatively small genome size and fully sequenced well-annotated genome. Today, the main regulators of DNA methylation are identified in rice. Moreover, compared to Arabidopsis, rice has an important evolutionary history due to human selection since its domestication. DNA methylation may be involved in both adaptation and agronomic performances and thus, a better understanding of epigenetic regulations in rice should contribute to improving the adaptation of crops to a changing environment. In this review, we expose the current knowledge on DNA methylation in rice and future perspectives to be considered. Full article

(This article belongs to the Special Issue Plant Epigenome Dynamics)

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