scholarly journals Mild drought induces phenotypic and DNA methylation plasticity but no transgenerational effects in Arabidopsis

2018 ◽  
Author(s):  
Tom JM Van Dooren ◽  
Amanda Bortolini Silveira ◽  
Elodie Gilbault ◽  
José M. Jiménez-Gómez ◽  
Antoine Martin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Environmental Changes ◽  
Trait Variation ◽  
Heritable Trait ◽  
Genome Bisulfite Sequencing ◽  
Successive Generations ◽  
Induced Changes ◽  
Heritable Effects ◽  
Mild Drought ◽  
Phenotypic Responses

SummaryWhether environmentally induced changes in phenotypes can be heritable is a topic with revived interest, in part because of observations in plants that heritable trait variation can occur without DNA sequence mutations. This other system of inheritance, called transgenerational epigenetics, typically involves differences in DNA methylation that are stable across multiple generations. However, it remains unknown if such a system responds to environmental changes and if it could therefore provide a rapid way for plants to generate adaptive heritable phenotypic variation. Here, we used a well-controlled phenotyping platform and whole-genome bisulfite sequencing to investigate potential heritable effects of mild drought applied over two successive generations in Arabidopsis thaliana. Plastic phenotypic responses were observed in plants exposed to drought. After an intervening generation without stress, descendants of stressed and non-stressed plants were phenotypically indistinguishable, except for very few trait-based parental effects, and irrespective of whether they were grown in control conditions or under water deficit. Moreover, while mild drought induced changes to the DNA methylome of exposed plants, DNA methylation variants were not inherited. These findings add to the growing body of evidence indicating that transgenerational epigenetics is not a common response of plants to environmental changes.

scholarly journals Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects

2020 ◽  
Vol 71 (12) ◽  
pp. 3588-3602 ◽  
Author(s):  
Tom J M Van Dooren ◽  
Amanda Bortolini Silveira ◽  
Elodie Gilbault ◽  
José M Jiménez-Gómez ◽  
Antoine Martin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Environmental Changes ◽  
Transgenerational Effects ◽  
Trait Variation ◽  
Genome Wide ◽  
Heritable Trait ◽  
Induced Changes ◽  
Plastic Responses ◽  
Mild Drought

Abstract There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown whether this alternative system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To assess potential transgenerational effects induced by the environment, we subjected four natural accessions of Arabidopsis thaliana together with the reference accession Col-0 to mild drought in a multi-generational experiment. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of the parental environments. However, after an intervening generation without stress, except for a very few trait-based parental effects, descendants of stressed and non-stressed plants were phenotypically indistinguishable irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, these variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects.

scholarly journals Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
David Secco ◽  
Chuang Wang ◽  
Huixia Shou ◽  
Matthew D Schultz ◽  
Serge Chiarenza ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Temporal Dynamics ◽  
Phosphate Starvation ◽  
A Genome ◽  
Genome Bisulfite Sequencing ◽  
Induced Genes ◽  
Spatio Temporal ◽  
Meiotic Transmission ◽  
Species Specific ◽  
Induced Changes

Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.

scholarly journals The epiallelic potential of transposable elements and its evolutionary significance in plants

2021 ◽  
Vol 376 (1826) ◽  
Author(s):  
Pierre Baduel ◽  
Vincent Colot
Keyword(s):  
Dna Methylation ◽  
Dna Sequence ◽  
Current Knowledge ◽  
Epigenetic Inheritance ◽  
Evolutionary Significance ◽  
Trait Variation ◽  
Heritable Trait ◽  
Epigenetic Machinery ◽  
Functional Consequences ◽  
The One

DNA provides the fundamental framework for heritability, yet heritable trait variation need not be completely ‘hard-wired’ into the DNA sequence. In plants, the epigenetic machinery that controls transposable element (TE) activity, and which includes DNA methylation, underpins most known cases of inherited trait variants that are independent of DNA sequence changes. Here, we review our current knowledge of the extent, mechanisms and potential adaptive contribution of epiallelic variation at TE-containing alleles in this group of species. For the purpose of this review, we focus mainly on DNA methylation, as it provides an easily quantifiable readout of such variation. The picture that emerges is complex. On the one hand, pronounced differences in DNA methylation at TE sequences can either occur spontaneously or be induced experimentally en masse across the genome through genetic means. Many of these epivariants are stably inherited over multiple sexual generations, thus leading to transgenerational epigenetic inheritance. Functional consequences can be significant, yet they are typically of limited magnitude and although the same epivariants can be found in nature, the factors involved in their generation in this setting remain to be determined. On the other hand, moderate DNA methylation variation at TE-containing alleles can be reproducibly induced by the environment, again usually with mild effects, and most of this variation tends to be lost across generations. Based on these considerations, we argue that TE-containing alleles, rather than their inherited epiallelic variants, are the main targets of natural selection. Thus, we propose that the adaptive contribution of TE-associated epivariation, whether stable or not, lies predominantly in its capacity to modulate TE mobilization in response to the environment, hence providing hard-wired opportunities for the flexible exploration of the phenotypic space. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

scholarly journals Identification of Putative Virulence Genes by DNA Methylation Studies in the Cereal Pathogen Fusarium graminearum

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1192
Author(s):  
Francesco Tini ◽  
Giovanni Beccari ◽  
Gianpiero Marconi ◽  
Andrea Porceddu ◽  
Micheal Sulyok ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fusarium Graminearum ◽  
Environmental Changes ◽  
Virulent Strain ◽  
Fungal Virulence ◽  
Wheat Seedlings ◽  
Wide Range ◽  
Conidia Production ◽  
Natural Hosts

DNA methylation mediates organisms’ adaptations to environmental changes in a wide range of species. We investigated if a such a strategy is also adopted by Fusarium graminearum in regulating virulence toward its natural hosts. A virulent strain of this fungus was consecutively sub-cultured for 50 times (once a week) on potato dextrose agar. To assess the effect of subculturing on virulence, wheat seedlings and heads (cv. A416) were inoculated with subcultures (SC) 1, 23, and 50. SC50 was also used to re-infect (three times) wheat heads (SC50×3) to restore virulence. In vitro conidia production, colonies growth and secondary metabolites production were also determined for SC1, SC23, SC50, and SC50×3. Seedling stem base and head assays revealed a virulence decline of all subcultures, whereas virulence was restored in SC50×3. The same trend was observed in conidia production. The DNA isolated from SC50 and SC50×3 was subject to a methylation content-sensitive enzyme and double-digest, restriction-site-associated DNA technique (ddRAD-MCSeEd). DNA methylation analysis indicated 1024 genes, whose methylation levels changed in response to the inoculation on a healthy host after subculturing. Several of these genes are already known to be involved in virulence by functional analysis. These results demonstrate that the physiological shifts following sub-culturing have an impact on genomic DNA methylation levels and suggest that the ddRAD-MCSeEd approach can be an important tool for detecting genes potentially related to fungal virulence.

scholarly journals Individuals Diagnosed with Binge-Eating Disorder Have DNA Hypomethylated Sites in Genes of the Metabolic System: A Pilot Study

Nutrients ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1413
Author(s):  
Mariana Lizbeth Rodríguez-López ◽  
José Jaime Martínez-Magaña ◽  
David Ruiz-Ramos ◽  
Ana Rosa García ◽  
Laura Gonzalez ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Eating Disorder ◽  
Protein Kinase ◽  
Binge Eating ◽  
Binge Eating Disorder ◽  
Environmental Changes ◽  
Diagnostic Category ◽  
The Body ◽  
Metabolic System ◽  
Genome Wide

Binge-eating disorder, recently accepted as a diagnostic category, is differentiated from bulimia nervosa in that the former shows the presence of binge-eating episodes and the absence of compensatory behavior. Epigenetics is a conjunct of mechanisms (like DNA methylation) that regulate gene expression, which are dependent on environmental changes. Analysis of DNA methylation in eating disorders shows that it is reduced. The present study aimed to analyze the genome-wide DNA methylation differences between individuals diagnosed with BED and BN. A total of 46 individuals were analyzed using the Infinium Methylation EPIC array. We found 11 differentially methylated sites between BED- and BN-diagnosed individuals, with genome-wide significance. Most of the associations were found in genes related to metabolic processes (ST3GAL4, PRKAG2, and FRK), which are hypomethylated genes in BED. Cg04781532, located in the body of the PRKAG2 gene (protein kinase AMP-activated non-catalytic subunit gamma 2), was hypomethylated in individuals with BED. Agonists of PRKAG2, which is the subunit of AMPK (AMP-activated protein kinase), are proposed to treat obesity, BED, and BN. The present study contributes important insights into the effect that BED could have on PRKAG2 activation.

scholarly journals Wild Zebrafish Sentinels: Biological Monitoring of Site Differences Using Behavior and Morphology

Toxics ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 165
Author(s):  
Jeffrey R. Kelly ◽  
Sierra G. Shelton ◽  
Danita K. Daniel ◽  
Anuradha Bhat ◽  
Rubina Mondal ◽  
...  
Keyword(s):  
Global Health ◽  
Environmental Changes ◽  
Rapid Assessment ◽  
Sexually Dimorphic ◽  
Plastic Pollution ◽  
Phenotypic Differences ◽  
Hypoxic Conditions ◽  
Body Shapes ◽  
Detection Evaluation ◽  
Phenotypic Responses

Environmental change poses a devastating risk to human and environmental health. Rapid assessment of water conditions is necessary for monitoring, evaluating, and addressing this global health danger. Sentinels or biological monitors can be deployed in the field using minimal resources to detect water quality changes in real time, quickly and cheaply. Zebrafish (Danio rerio) are ideal sentinels for detecting environmental changes due to their biomedical tool kit, widespread geographic distribution, and well-characterized phenotypic responses to environmental disturbances. Here, we demonstrate the utility of zebrafish sentinels by characterizing phenotypic differences in wild zebrafish between two field sites in India. Site 1 was a rural environment with flowing water, low-hypoxic conditions, minimal human-made debris, and high iron and lead concentrations. Site 2 was an urban environment with still water, hypoxic conditions, plastic pollution, and high arsenic, iron, and chromium concentrations. We found that zebrafish from Site 2 were smaller, more cohesive, and less active than Site 1 fish. We also found sexually dimorphic body shapes within the Site 2, but not the Site 1, population. Advancing zebrafish sentinel research and development will enable rapid detection, evaluation, and response to emerging global health threats.

106 The Effects of Fetal Programming on Offspring Pancreas DNA Methylation

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 54-55
Author(s):  
Maria L Hoffman
Keyword(s):  
Dna Methylation ◽  
Fetal Programming ◽  
Maternal Nutrition ◽  
Maternal Diet ◽  
Multiple Generations ◽  
Livestock Species ◽  
Maternal Programming ◽  
Genome Bisulfite Sequencing ◽  
The Many ◽  
Methylation Patterns

Abstract It has been well documented that fetal programming, caused by changes to the maternal environment during pregnancy, can impact the overall health and growth of the offspring in livestock and non-livestock species alike. These effects are observed in the F1 offspring as well as across subsequent generations; however, the mechanisms by which this occurs are still poorly understood. Epigenetics is one of the many mechanisms that is hypothesized to have a role in fetal programming and may be mediating the observed effects across multiple generations. It has been demonstrated by others that DNA methylation patterns can be altered by an individuals’ diet and that the pancreas is vulnerable to the effects of fetal programming. Therefore, we evaluated the effects of poor maternal nutrition during gestation on the pancreas tissue of lambs. We have demonstrated that maternal under- or overnutrition during gestation alters the DNA methylation patterns of the offspring pancreas tissue with these effects being diet dependent and sex specific. We have also begun evaluating the effects of maternal diet in murine models using whole-genome bisulfite sequencing to compare species differences and determine if there are any changes conserved across species. This will allow us to focus on a smaller number of critical factors in individuals as they age and across multiple generations in livestock species such as sheep and cattle. From these data we will be able to elucidate the role DNA methylation has in mediating the effects of maternal programming in the pancreas tissue.

scholarly journals A high-altitude peatland record of environmental changes in the NW Argentine Andes (24 ° S) over the last 2100 years

2016 ◽  
Vol 12 (5) ◽  
pp. 1165-1180 ◽  
Author(s):  
Karsten Schittek ◽  
Sebastian T. Kock ◽  
Andreas Lücke ◽  
Jonathan Hense ◽  
Christian Ohlendorf ◽  
...  
Keyword(s):  
High Altitude ◽  
Environmental Changes ◽  
Regional Scale ◽  
Central Andes ◽  
High Accumulation ◽  
Climate Conditions ◽  
Climate Anomalies ◽  
Dry Conditions ◽  
Induced Changes ◽  
The 19Th Century

Abstract. High-altitude cushion peatlands are versatile archives for high-resolution palaeoenvironmental studies, due to their high accumulation rates, range of proxies, and sensitivity to climatic and/or human-induced changes. Especially within the Central Andes, the knowledge about climate conditions during the Holocene is limited. In this study, we present the environmental and climatic history for the last 2100 years of Cerro Tuzgle peatland (CTP), located in the dry Puna of NW Argentina, based on a multi-proxy approach. X-ray fluorescence (XRF), stable isotope and element content analyses (δ13C, δ15N, TN and TOC) were conducted to analyse the inorganic geochemistry throughout the sequence, revealing changes in the peatlands' past redox conditions. Pollen assemblages give an insight into substantial environmental changes on a regional scale. The palaeoclimate varied significantly during the last 2100 years. The results reflect prominent late Holocene climate anomalies and provide evidence that in situ moisture changes were coupled to the migration of the Intertropical Convergence Zone (ITCZ). A period of sustained dry conditions prevailed from around 150 BC to around AD 150. A more humid phase dominated between AD 200 and AD 550. Afterwards, the climate was characterised by changes between drier and wetter conditions, with droughts at around AD 650–800 and AD  1000–1100. Volcanic forcing at the beginning of the 19th century (1815 Tambora eruption) seems to have had an impact on climatic settings in the Central Andes. In the past, the peatland recovered from climatic perturbations. Today, CTP is heavily degraded by human interventions, and the peat deposit is becoming increasingly susceptible to erosion and incision.

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