scholarly journals Changes of gene expression but not cytosine methylation are associated with male parental care reflecting behavioural state, social context and individual flexibility

2018 ◽  
Vol 222 (2) ◽  
pp. jeb188649 ◽  
Author(s):  
Christopher B. Cunningham ◽  
Lexiang Ji ◽  
Elizabeth C. McKinney ◽  
Kyle M. Benowitz ◽  
Robert J. Schmitz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Social Context ◽  
Parental Care ◽  
Cytosine Methylation ◽  
Behavioural State

scholarly journals Changes of gene expression but not cytosine methylation are associated with plasticity of male parental care reflecting behavioural state, social context, and individual flexibility

2017 ◽  
Author(s):  
CB Cunningham ◽  
L Ji ◽  
EC McKinney ◽  
KM Benowitz ◽  
RJ Schmitz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Social Context ◽  
Parental Care ◽  
Individual Variation ◽  
Molecular Mechanisms ◽  
Cytosine Methylation ◽  
Burying Beetle ◽  
Behavioural State ◽  
Age Related

AbstractBehaviour is often on the front line of plasticity in response to different environments. At the genetic level, behavioural changes are likely to be associated with changes of gene expression. Most studies to date have focused on gene expression differences associated with discrete behavioural states reflecting development or age-related changes, such as honey bee castes. However, more rapidly flexible behaviour is often observed in response to social context or simple individual variation. The differences in genetic influences for the different forms of plasticity are poorly understood. In this study we contrasted gene expression during male parental care of the burying beetle, Nicrophorus vespilloides, in a factorial design. Male N. vespilloides males typically do not provide care when females are present. However, male care is inducible by the removing female and has parental effects equivalent to female care. We used this experimental manipulation to isolate gene expression and cytosine methylation associated with differences of behavioural state, differences of social context, or differences of individual flexibility for expressing care. The greatest number of differentially expressed genes was associated with behavioural state, followed by differences of social contexts, and lastly differences of individual variation. DNA methylation has been hypothesized to regulate the transcriptional architecture that regulates behavioural transitions. We tested this hypothesis by quantifying differences of cytosine methylation that were associated with differences of behavioural state and individual flexibility. Changes of cytosine methylation were not associated with changes of gene expression. Our results suggest a hierarchical association between gene expression and the different sources of variation that influence behaviour, but that this process is not controlled by DNA methylation despite reflecting levels of plasticity in behaviour. Our results further suggest that the extent that a behaviour is transient plays an underappreciated role in determining the molecular mechanisms that underpin the behaviour.

Different roles for cytosine methylation in HLA class ii gene expression

1985 ◽  
Vol 22 (5) ◽  
pp. 427-440 ◽  
Author(s):  
Fred Levine ◽  
Donald Pious
Keyword(s):  
Gene Expression ◽  
Cytosine Methylation ◽  
Class Ii ◽  
Hla Class Ii

scholarly journals Gene body methylation mediates epigenetic inheritance of plant traits

2021 ◽  
Author(s):  
Zaigham Shahzad ◽  
Jonathan D. Moore ◽  
Daniel Zilberman
Keyword(s):  
Gene Expression ◽  
Flowering Time ◽  
Cytosine Methylation ◽  
Plant Traits ◽  
Phenotypic Diversity ◽  
Strong Association ◽  
Epigenetic Inheritance ◽  
Evolutionary Significance ◽  
Gene Body ◽  
Gene Body Methylation

AbstractCytosine methylation is an epigenetically heritable DNA modification common in plant and animal genes, but the functional and evolutionary significance of gene body methylation (gbM) has remained enigmatic. Here we show that gbM enhances gene expression in Arabidopsis thaliana. We also demonstrate that natural gbM variation influences drought and heat tolerance and flowering time by modulating gene expression, including that of Flowering Locus C (FLC). Notably, epigenetic variation accounts for as much trait heritability in natural populations as DNA sequence polymorphism. Furthermore, we identify gbM variation in numerous genes associated with environmental variables, including a strong association between flowering time, spring atmospheric NO2 – a by-product of fossil fuel burning – and FLC epialleles. Our study demonstrates that gbM is an important modulator of gene expression, and its natural variation fundamentally shapes phenotypic diversity in plant populations. Thus, gbM provides an epigenetic basis for adaptive evolution independent of genetic polymorphism.

scholarly journals Silencing of Mutator Elements in Maize Involves Distinct Populations of Small RNAs and Distinct Patterns of DNA Methylation

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 379-391 ◽  
Author(s):  
Diane Burgess ◽  
Hong Li ◽  
Meixia Zhao ◽  
Sang Yeol Kim ◽  
Damon Lisch
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Small Rnas ◽  
Cytosine Methylation ◽  
De Novo ◽  
Epigenetic Silencing ◽  
Inverted Repeats ◽  
Causal Relationships ◽  
Terminal Inverted Repeats ◽  
Silencing Pathways

Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they post to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species often have dramatically different populations of TEs, suggesting periodic rounds of activity and silencing. Here, we show that the process of de novo methylation of an active element in maize involves two distinct pathways, one of which is directly implicated in causing epigenetic silencing and one of which is the result of that silencing. Epigenetic changes involve changes in gene expression that can be heritably transmitted to daughter cells in the absence of changes in DNA sequence. Epigenetics has been implicated in phenomena as diverse as development, stress response, and carcinogenesis. A significant challenge facing those interested in investigating epigenetic phenomena is determining causal relationships between DNA methylation, specific classes of small RNAs, and associated changes in gene expression. Because they are the primary targets of epigenetic silencing in plants and, when active, are often targeted for de novo silencing, TEs represent a valuable source of information about these relationships. We use a naturally occurring system in which a single TE can be heritably silenced by a single derivative of that TE. By using this system it is possible to unravel causal relationships between different size classes of small RNAs, patterns of DNA methylation, and heritable silencing. Here, we show that the long terminal inverted repeats within Zea mays MuDR transposons are targeted by distinct classes of small RNAs during epigenetic silencing that are dependent on distinct silencing pathways, only one of which is associated with transcriptional silencing of the transposon. Further, these small RNAs target distinct regions of the terminal inverted repeats, resulting in different patterns of cytosine methylation with different functional consequences with respect to epigenetic silencing and the heritability of that silencing.

Changes of cytosine methylation induced by wide hybridization and allopolyploidy in Cucumis

Genome ◽  
2008 ◽  
Vol 51 (10) ◽  
pp. 789-799 ◽  
Author(s):  
Longzheng Chen ◽  
Jinfeng Chen
Keyword(s):  
Gene Expression ◽  
Cytosine Methylation ◽  
Polymerase Chain Reaction Analysis ◽  
Methylation Pattern ◽  
Functional Genes ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Phenotypic Variations ◽  
Parent Observations ◽  
Or Genes

We previously demonstrated that allopolyploidization could induce phenotypic variations and genome changes in a newly synthesized allotetraploid in Cucumis . To explore the molecular involvement of epigenetic phenomena, we investigated cytosine methylation in Cucumis by using methylation-sensitive amplified polymorphism (MSAP). Results revealed a twofold difference in the level of cytosine methylation between the reciprocal F1 hybrids and the allotetraploid. Analysis of the methylation pattern indicated that methylation changed at 2.0% to 6.4% of total sites in both the F1 hybrids and the allotetraploid compared with their corresponding parents. Furthermore, 68.2% to 80.0% of the changed sites showed an increase in cytosine methylation and a majority of the methylated sites were from the maternal parent. Observations in different generations of the allotetraploid found that the extent of change in cytosine methylation pattern between the S1 and S2 was significantly higher than that between the S2 and S3, suggesting stability in advanced generations. Analysis of 7 altered sequences indicated their similarity to known functional genes or genes involved in regulating gene expression. Reverse transcription – polymerase chain reaction analysis suggested that at least two of the methylation changes might be related to gene expression changes, which further supports the hypothesis that DNA methylation plays a significant role in allopolyploidization.

scholarly journals The Role of Epigenetic Alterations in Papillary Thyroid Carcinogenesis

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Ogechukwu P. Eze ◽  
Lee F. Starker ◽  
Tobias Carling
Keyword(s):  
Gene Expression ◽  
Cytosine Methylation ◽  
Cpg Islands ◽  
Tumor Development ◽  
Genetic Alterations ◽  
Papillary Thyroid ◽  
Promoter Regions ◽  
Novel Technologies ◽  
Approaches To Study ◽  
Thyroid Malignancies

Papillary thyroid carcinoma (PTC) accounts for over 80% of all thyroid malignancies. The molecular pathogenesis remains incompletely clarified although activation of the RET fusion oncogenes, and RAS and BRAF oncogenes, has been well characterized. Novel technologies using genome-wide approaches to study tumor genomes and epigenomes have provided great insights into tumor development. Growing evidence shows that acquired epigenetic abnormalities participate with genetic alterations to cause altered patterns of gene expression/function. It has been established beyond doubt that promoter cytosine methylation in CpG islands, and the subsequent gene silencing, is intimately involved in cancer development. These epigenetic events very likely contribute to significant variation in gene expression profiling, phenotypic features, and biologic characteristics seen in PTC. Hypermethylation of promoter regions has also been analyzed in PTC, and most studies have focused on individual genes or a small cohort of genes implicated in tumorigenesis.

scholarly journals The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with gene expression in sesame

2018 ◽  
Author(s):  
Komivi Dossa ◽  
Marie Ali Mmadi ◽  
Rong Zhou ◽  
Qi Zhou ◽  
Mei Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Abiotic Stresses ◽  
Cytosine Methylation ◽  
De Novo ◽  
Recovery Phase ◽  
Epigenetic Mechanism ◽  
Drought Tolerant ◽  
Sesame Genotypes ◽  
Methylation Patterns

AbstractDNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum L.) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, a property attributed to its presumed origin in Africa or India. Understanding DNA methylation patterns in sesame under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying its contrasting responses to these principal abiotic stresses. Here, we combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, gene expression alteration, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes under control, stress and recovery conditions. Our data showed that drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging decreased the level of methylation under stress but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the differentially expressed genes (DEGs) were highly correlated with the methylation patterns. We observed that DM was associated with the up-regulation of the DEGs while DNM was correlated with the down-regulation of the DEGs. In addition, we sequenced 44 differentially methylated regions of which 90% overlapped with the promoters and coding sequences of the DEGs. Altogether, we demonstrated that sesame has divergent epigenetic programs that respond to drought and waterlogging stresses. Our results also highlighted the possible interplay among DNA methylation and gene expression, which may modulate the contrasting responses to drought and waterlogging in sesame.

scholarly journals Integrative Network Analysis of Differentially Methylated and Expressed Genes for Biomarker Identification in Leukemia

2019 ◽  
Author(s):  
Robersy Sanchez ◽  
Sally A. Mackenzie
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Cytosine Methylation ◽  
Complex Disease ◽  
Lymphoblastic Leukemia ◽  
Integrated Analysis ◽  
Ras Signaling ◽  
Protein Protein Interaction ◽  
Diagnosis And Prognosis ◽  
Ppi Networks

AbstractGenome-wide DNA methylation and gene expression are commonly altered in pediatric acute lymphoblastic leukemia (PALL). Integrated analysis of cytosine methylation and expression datasets has the potential to provide deeper insights into the complex disease states and their causes than individual disconnected analyses. Studies of protein-protein interaction (PPI) networks of differentially methylated (DMGs) and expressed genes (DEGs) showed that gene expression and methylation consistently targeted the same gene pathways associated with cancer: Pathways in cancer, Ras signaling pathway, PI3K-Akt signaling pathway, and Rap1 signaling pathway, among others. Detected gene hubs and hub sub-networks are integrated by signature loci associated with cancer that include, for example, NOTCH1, RAC1, PIK3CD, BCL2, and EGFR. Statistical analysis disclosed a stochastic deterministic dependence between methylation and gene expression within the set of genes simultaneously identified as DEGs and DMGs, where larger values of gene expression changes are probabilistically associated with larger values of methylation changes. Concordance analysis of the overlap between enriched pathways in DEG and DMG datasets revealed statistically significant agreement between gene expression and methylation changes, reflecting a coordinated response of methylation and gene-expression regulatory systems. These results support the identification of reliable and stable biomarkers for cancer diagnosis and prognosis.

scholarly journals Distinct Cytosine Modification Profiles Define Epithelial-to-Mesenchymal Cell-State Transitions

2021 ◽  
Author(s):  
Min Kyung Lee ◽  
Meredith S. Brown ◽  
Owen Wilkins ◽  
Diwakar R. Pattabiraman ◽  
Brock C. Christensen
Keyword(s):  
Gene Expression ◽  
Cytosine Methylation ◽  
Epithelial To Mesenchymal Transition ◽  
Mesenchymal Cell ◽  
State Transitions ◽  
Open Chromatin ◽  
Intermediate Cell ◽  
Mesenchymal Transition ◽  
Accessible Chromatin ◽  
Cytosine Modification

Abstract Background: Epithelial-to-mesenchymal transition (EMT) is an early step in the invasion-metastasis cascade, involving progression through a number of cell intermediate states. Due to challenges with isolating intermediate cell states in EMT, genome-wide cytosine modification mechanisms that define transition through EMT states are not completely understood. We measured multiple DNA cytosine methylation modification marks, complemented with chromatin accessibility and gene expression, across clonal populations residing in specific EMT states. Results: Clones exhibiting intermediate EMT phenotypes demonstrated increased global 5-hydroxymethylcytosine (5hmC), decreased 5-methylcytosine (5mC), and more accesible chromatin. Open chromatin regions containing CpG loci with abundant 5hmC were enriched in motifs of key EMT transcription factors, ZEB1 and Snail. The magnitude of altered gene expression in intermediate cell states was higher for genes both with increased gene promoter 5hmC and differentially accessible chromatin compared with genes that exhibited differentially accessible chromatin alone, implicating functional epigenetic duality in regulation of EMT.Conclusion: Our results indicate the importance of both distinct and shared epigenetic profiles at the cytosine and chromatin level associated with EMT processes that contribute to gene regulation and which may be targeted to prevent the progression of EMT.

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