230: Maternal diet-induced changes in DNA methylation precede gene expression changes in liver

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 to 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 assess 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 tissue specific. DMMs were mostly located in close proximity to repeat elements but also 1094 genes, of which many possessed GO terms associated with plant responses to stress. Identified markers identified have potential value as sentinels of salt stress and provide a start point to understand the functional role of DNA methylation in facilitating barley’s response to this stressor.

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

10.20944/preprints201804.0323.v2 ◽

2018 ◽

Cited By ~ 1

Author(s):

Moumouni Konaté ◽

Michael J. Wilkinson ◽

Benjamin T. Mayne ◽

Stephen M. Pederson ◽

Eileen S. Scott ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Salt Stress ◽

Growth And Yield ◽

Plant Responses ◽

Global Methylation ◽

Repeat Elements ◽

Starting Point ◽

Induced Changes

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.

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

Journal of Experimental Botany ◽

10.1093/jxb/eraa132 ◽

2020 ◽

Vol 71 (12) ◽

pp. 3588-3602 ◽

Cited By ~ 3

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.

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Context is King — Questioning the causal role of DNA methylation in environmentally induced changes in gene expression

Current Opinion in Toxicology ◽

10.1016/j.cotox.2019.08.003 ◽

2019 ◽

Vol 14 ◽

pp. 46-51

Author(s):

Yudhishtar Bedi ◽

Michael C. Golding

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Causal Role ◽

Induced Changes

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Maternal diet as a modifier of offspring epigenetics

Journal of Developmental Origins of Health and Disease ◽

10.1017/s2040174415000124 ◽

2015 ◽

Vol 6 (2) ◽

pp. 88-95 ◽

Cited By ~ 53

Author(s):

K. A. Lillycrop ◽

G. C. Burdge

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Early Life ◽

Disease Risk ◽

Important Determinant ◽

Maternal Diet ◽

Substantial Body ◽

Highly Sensitive ◽

Non Coding Rnas ◽

Epigenetic Processes

There has been a substantial body of evidence, which has shown that genetic variation is an important determinant of disease risk. However, there is now increasing evidence that alterations in epigenetic processes also play a role in determining susceptibility to disease. Epigenetic processes, which include DNA methylation, histone modifications and non-coding RNAs play a central role in regulating gene expression, determining when and where a gene is expressed as well as the level of gene expression. The epigenome is highly sensitive to a variety of environmental factors, especially in early life. One factor that has been shown consistently to alter the epigenome is maternal diet. This review will focus on how maternal diet can modify the epigenome of the offspring, producing different phenotypes and altered disease susceptibilities.

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Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)

10.1101/2020.06.05.136424 ◽

2020 ◽

Author(s):

Alan M. Downey-Wall ◽

Louise P. Cameron ◽

Brett M. Ford ◽

Elise M. McNally ◽

Yaamini R. Venkataraman ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Crassostrea Virginica ◽

Gene Clusters ◽

Eastern Oyster ◽

Gene Body ◽

Mantle Tissue ◽

Molecular Responses ◽

Extrapallial Fluid ◽

Induced Changes

AbstractEarly evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in the Eastern oyster (Crassostrea virginica) exposed to experimental OA over 80 days. Oysters were reared under three experimental pCO2 treatments (‘control’, 580 μatm; ‘moderate OA’, 1000 uatm; ‘high OA’, 2800 μatm) and sampled at 6 time points (24 hours - 80 days). We found that high OA initially induced changes in the pH of the extrapallial fluid (pHEPF) relative to the external seawater, but the magnitude of this difference was highest at 9 days and diminished over time. Calcification rates were significantly lower in the high OA treatment compared to the other treatments. To explore how oysters regulate their extrapallial fluid, gene expression and DNA methylation were examined in the mantle-edge tissue of oysters from day 9 and 80 in the control and high OA treatments. Mantle tissue mounted a significant global molecular response (both in the transcriptome and methylome) to OA that shifted through time. Although we did not find individual genes that were significantly differentially expressed to OA, the pHEPF was correlated with the eigengene expression of several co-expressed gene clusters. A small number of OA-induced differentially methylated loci were discovered, which corresponded with a weak association between OA-induced changes in genome-wide gene body DNA methylation and gene expression. Gene body methylation, however, was not significantly correlated with the eigengene expression of pHEPF correlated gene clusters. These results suggest that in C. virginica, OA induces a subtle response in a large number of genes, but also indicates that plasticity at the molecular level may be limited. Our study highlights the need to re-assess the plasticity of tissue-specific molecular responses in marine calcifiers, as well as the role of DNA methylation and gene expression in mediating physiological and biomineralization responses to OA.

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Maternal Low-Fat Diet Programs the Hepatic Epigenome despite Exposure to an Obesogenic Postnatal Diet

Nutrients ◽

10.3390/nu11092075 ◽

2019 ◽

Vol 11 (9) ◽

pp. 2075 ◽

Cited By ~ 3

Author(s):

Laura Moody ◽

Justin Shao ◽

Hong Chen ◽

Yuan-Xiang Pan

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Early Life ◽

Maternal Diet ◽

Sprague Dawley ◽

Low Fat ◽

Cancer Pathways ◽

Low Fat Diet ◽

Contact Data ◽

Obesogenic Diet

Obesity and metabolic disease present a danger to long-term health outcomes. It has been hypothesized that epigenetic marks established during early life might program individuals and have either beneficial or harmful consequences later in life. In the present study, we examined whether maternal diet alters DNA methylation and whether such modifications persist after an obesogenic postnatal dietary challenge. During gestation and lactation, male Sprague-Dawley rats were exposed to either a high-fat diet (HF; n = 10) or low-fat diet (LF; n = 10). After weaning, all animals were fed a HF diet for an additional nine weeks. There were no differences observed in food intake or body weight between groups. Hepatic DNA methylation was quantified using both methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq). Overall, 1419 differentially methylated regions (DMRs) were identified. DMRs tended to be located in CpG shores and were enriched for genes involved in metabolism and cancer. Gene expression was measured for 31 genes in these pathways. Map3k5 and Igf1r were confirmed to be differentially expressed. Finally, we attempted to quantify the functional relevance of intergenic DMRs. Using chromatin contact data, we saw that conserved DMRs were topologically associated with metabolism genes, which were associated with differential expression of Adh5, Enox1, and Pik3c3. We show that although maternal dietary fat is unable to reverse offspring weight gain in response to a postnatal obesogenic diet, early life diet does program the hepatic methylome. Epigenetic alterations occur primarily in metabolic and cancer pathways and are associated with altered gene expression, but it is unclear whether they bear consequence later in life.

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