Characterization of Epigenetic Biomarkers Using New Molecular Approaches

Gentil, Marie-Véronique; Maury, Stéphane

doi:10.1007/978-1-4020-6295-7_16

Cited by 11 publications

(8 citation statements)

References 55 publications

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“…Recent reports describe the use of several different approaches for the identification of epialleles during plant culture in vitro (Berdasco et al , Miguel and Marum , Maury et al ). The use of high‐throughput genome technologies will accelerate the release of complete genome sequences for trees such as hybrid larch, and this may lead to a better understanding of biological processes as well as the validation of global DNA methylation variations reported in this study and the identification of epigenetic markers (Gentil and Maury , Johannes et al , Miguel and Marum ). Studying the latter aspect is particularly relevant, since cell‐to‐cell variation in methylation has already been observed in callus, the epiallelic variants being transmitted to regenerated plants and fixed (Krisova et al 2009, Jaligot et al ).…”

Section: Discussionmentioning

confidence: 91%

In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses

Teyssier¹,

Maury

Beaufour

et al. 2013

Physiologia Plantarum

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A global DNA methylation and proteomics approach was used to investigate somatic embryo maturation in hybrid larch. Each developmental step during somatic embryogenesis was associated with a distinct and significantly different global DNA methylation level: from 45.8% mC for undifferentiated somatic embryos (1-week proliferation) to 61.5% mC for immature somatic embryos (1-week maturation), while maturation was associated with a decrease in DNA methylation to 53.4% for mature cotyledonary somatic embryos (8-weeks maturation). The presence of 5-azacytidine (hypo-methylating agent) or hydroxyurea (hyper-methylating agent) in the maturation medium altered the global DNA methylation status of the embryogenic cultures, and significantly reduced both their relative growth rate and embryogenic potential, suggesting an important role for DNA methylation in embryogenesis. Maturation was also assessed by examining changes in the total protein profile. Storage proteins, identified as legumin- and vicilin-like, appeared at the precotyledonary stage. In the proteomic study, total soluble proteins were extracted from embryos after 1 and 8 weeks of maturation, and separated by two-dimensional gel electrophoresis. There were 147 spots which showed significant differences between the stages of maturation; they were found to be involved mainly in primary metabolism and the stabilization of the resulting metabolites. This indicated that the somatic embryo was still metabolically active at 8 weeks of maturation. This is the first report of analyses of global DNA methylation (including the effects of hyper- and hypo-treatments) and proteome during somatic embryogenesis in hybrid larch, and thus provides novel insights into maturation of conifer somatic embryos.

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Section: Discussionmentioning

confidence: 91%

In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses

Teyssier¹,

Maury

Beaufour

et al. 2013

Physiologia Plantarum

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“…Nevertheless, considering the role of DNA methylation in the fine-tuning control of gene expression, we hypothesise that epigenetic traits may be determinants of poplar productivity. The identification of the genomic sequences that show differential methylation should now be envisaged using recently published approaches (Gentil and Maury, 2007;Zhang et al, 2006). This will permit the discovery of biomarkers that could represent valuable tools for poplar breeders.…”

Section: Epigenetic Traits Scaled With Morphological Traitsmentioning

confidence: 99%

DNA methylation and histone acetylation: genotypic variations in hybrid poplars, impact of water deficit and relationships with productivity

et al. 2010

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Keywords: methylcytosine / shoot apex / vegetative development / water deficit / productivity Abstract • Several reports on annual plants have already shown the involvement of epigenetic modifiers such as DNA methylation in their adaptation to abiotic stresses.• Nevertheless, the genotypic variations of epigenetic modifiers, their possible correlations with morphological traits and the impact of water deficit have not been described for perennial plants.• Six genotypes of Populus deltoides × P. nigra were subjected or not to a moderate water deficit treatment. Various morphological traits such as the height of the plants, their biomass and the total leaf area were measured to characterize the productivity in both conditions. Levels of DNA methylation, histone acetylation and the activities and isoform accumulation of the corresponding enzymes were measured at the shoot apex, the site of morphogenesis. Genotypic variation was observed for the morphological traits and the epigenetic variables and correlations were established among them. Genotypic variation for DNA methylation was detected in hybrid poplars. A positive correlation was demonstrated between DNA methylation percentage and productivity under well watered conditions.• While there was a general decrease of growth for all genotypes in response to a moderate water deficit, genotypic dependant variations of DNA methylation were found suggesting different strategies among hybrids. Mots-clés : Résumé -Méthylation de l'ADN et acétylation des histones : variations génotypiques chez des peupliers hybrides, impact d'un déficit hydrique et relations avec la productivité.• Plusieurs études sur des plantes annuelles ont déjà montré l'implication des modifications épi-génétiques telles que la méthylation de l'ADN dans la plasticité de leurs réponses aux contraintes abiotiques.• Néanmoins, les variations génotypiques de ces modifications épigénétiques, leur possible corréla-tion avec des variables de croissance et l'impact d'un déficit hydrique n'ont pas été décrits sur une plante pérenne.• Six génotypes de Populus deltoïdes × P. nigra ont été soumis ou non à un déficit hydrique modéré et plusieurs variables de croissance ont été mesurées afin de caractériser leur productivité. Les niveaux de méthylation de l'ADN, d'acétylation des histones, les activités enzymatiques et l'accumulation des isoformes correspondantes ont été mesurés sur des apex caulinaires, site de la morphogenèse. Des variations génotypiques ont été observées pour les variables de croissance et épigénétiques. Une corrélation positive a été mise en évidence entre la méthylation de l'ADN et la productivité en condition hydrique favorable.• Bien qu'il y ait une diminution générale de la croissance de tous les génotypes en réponse à un défi-cit hydrique modéré, des variations génotype-dépendant de la méthylation de l'ADN ont été trouvées suggérant différentes stratégies entre hybrides.

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“…The general model for de novo organogenesis under controlled conditions has been outlined in Arabidopsis for the acquisition of cell pluripotency (Gentil and Maury 2007, Berdasco et al 2008, Zhao et al 2008, Miguel and Marum 2011). Nevertheless, little is known about (1) the functional role of gene regulation by DNA methylation during in vitro organogenesis, (2) how different organs can be regenerated from the same explants under different conditions and (3) the possibility to use molecular markers to improve in vitro technologies applied to crop plants.…”

Section: Introductionmentioning

confidence: 99%

Genic DNA methylation changes during in vitro organogenesis: organ specificity and conservation between parental lines of epialleles

Maury

Trap-Gentil

Hébrard

et al. 2012

Physiologia Plantarum

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During differentiation, in vitro organogenesis calls for the adjustment of the gene expression program toward a new fate. The role of epigenetic mechanisms including DNA methylation is suggested but little is known about the loci affected by DNA methylation changes, particularly in agronomic plants for witch in vitro technologies are useful such as sugar beet. Here, three pairs of organogenic and non-organogenic in vitro cell lines originating from different sugar beet (Beta vulgaris altissima) cultivars were used to assess the dynamics of DNA methylation at the global or genic levels during shoot or root regeneration. The restriction landmark genome scanning for methylation approach was applied to provide a direct quantitative epigenetic assessment of several CG methylated genes without prior knowledge of gene sequence that is particularly adapted for studies on crop plants without a fully sequenced genome. The cloned sequences had putative roles in cell proliferation, differentiation or unknown functions and displayed organ-specific DNA polymorphism for methylation and changes in expression during in vitro organogenesis. Among them, a potential ubiquitin extension protein 6 (UBI6) was shown, in different cultivars, to exhibit repeatable variations of DNA methylation and gene expression during shoot regeneration. In addition, abnormal development and callogenesis were observed in a T-DNA insertion mutant (ubi6) for a homologous sequence in Arabidopsis. Our data showed that DNA methylation is changed in an organ-specific way for genes exhibiting variations of expression and playing potential role during organogenesis. These epialleles could be conserved between parental lines opening perspectives for molecular markers.

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Characterization of Epigenetic Biomarkers Using New Molecular Approaches

Cited by 11 publications

References 55 publications

In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses

In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses

DNA methylation and histone acetylation: genotypic variations in hybrid poplars, impact of water deficit and relationships with productivity

Genic DNA methylation changes during in vitro organogenesis: organ specificity and conservation between parental lines of epialleles

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