scholarly journals Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

2021 ◽  
Author(s):  
Zhikai Liang ◽  
Sarah N Anderson ◽  
Jaclyn M Noshay ◽  
Peter A Crisp ◽  
Tara A Enders ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Leaf Tissue ◽  
Inbred Lines ◽  
Stress Conditions ◽  
The Other ◽  
Epigenetic Variation ◽  
Genome Wide ◽  
Repetitive Nature ◽  
The Family

Abstract Transposable elements (TEs) pervade most eukaryotic genomes. The repetitive nature of TEs complicates the analysis of their expression. Evaluation of the expression of both TE families (using unique and multi-mapping reads) and specific elements (using uniquely mapping reads) in leaf tissue of three maize (Zea mays) inbred lines subjected to heat or cold stress reveals no evidence for genome-wide activation of TEs, however some specific TE families generate transcripts only in stress conditions. There is substantial variation for which TE families exhibit stress-responsive expression in the different genotypes. In order to understand the factors that drive expression of TEs, we focused on a subset of families in which we could monitor expression of individual elements. The stress-responsive activation of a TE family can often be attributed to a small number of elements in the family that contain regions lacking DNA methylation. Comparisons of the expression of TEs in different genotypes revealed both genetic and epigenetic variation. Many of the specific TEs that are activated in stress in one inbred are not present in the other inbred, explaining the lack of activation. Among the elements that are shared in both genomes but only expressed in one genotype, we found that many exhibit differences in DNA methylation such that the genotype without expression is fully methylated. This study provides insights into the regulation of expression of TEs in normal and stress conditions and highlights the role of chromatin variation between elements in a family or between genotypes for contributing to expression variation. The highly repetitive nature of many transposable elements (TEs) complicates the analysis of their expression. Although most TEs are not expressed, some exhibit expression in certain tissues or conditions. We monitored the expression of both TE families (using unique and multi-mapping reads) and specific elements (using uniquely mapping reads) in leaf tissue of three maize (Zea mays) inbred lines subjected to heat or cold stress. While genome-wide activation of TEs did not occur, some TE families generated transcripts only in stress conditions with variation by genotype. To better understand the factors that drive expression of TEs, we focused on a subset of families in which we could monitor expression of individual elements. In most cases stress-responsive activation of a TE family was attributed to a small number of elements in the family. The elements that contained small regions lacking DNA methylation regions showed enriched expression while fully methylated elements were rarely expressed in control or stress conditions. The cause of varied expression in the different genotypes was due to both genetic and epigenetic variation. Many specific TEs activated by stress in one inbred were not present in the other inbred. Among the elements shared in both genomes, full methylation inhibited expression in one of the genotypes. This study provides insights into the regulation of TE expression in normal and stress conditions and highlights the role of chromatin variation between elements in a family or between genotypes for contributing to expression.

scholarly journals Genetic and epigenetic contributions to variation in transposable element expression responses to abiotic stress in maize

2020 ◽  
Author(s):  
Zhikai Liang ◽  
Sarah N. Anderson ◽  
Jaclyn M. Noshay ◽  
Peter A. Crisp ◽  
Tara A. Enders ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Abiotic Stress ◽  
Leaf Tissue ◽  
Stress Conditions ◽  
List Type ◽  
Genome Wide ◽  
Maize Genotypes ◽  
Repetitive Nature ◽  
A Genome ◽  
The Family

SummaryTransposable elements (TEs) pervade most eukaryotic genomes but the repetitive nature of TEs has complicated the analysis of their expression. Although the majority of TEs are silent, we document the activation of some TEs during abiotic stress.TE expression was monitored in seedling leaf tissue of maize inbreds subjected to heat or cold stress conditions. DNA methylation profiles and comparative genomics were used to probe the variability of TE expression responses.Although there was no evidence for a genome-wide activation of TEs, a subset of TE families generate transcripts only in stress conditions. There is substantial variation for which TE families exhibit stress-responsive expression in the three genotypes. The stress-responsive activation of a TE family can often be attributed to a small number of elements in the family. These elements that are activated often contain small regions lacking DNA methylation, while fully methylated elements are rarely expressed. A comparison of the expression of specific TEs in different maize genotypes reveals high levels of variability that can be attributed to both genome content differences and epigenetic variation.This study provides insights into the genetic and epigenetic factors that influence TE regulation in normal and stress conditions.

DDR1 methylation is associated with bipolar disorder and the isoform expression and methylation of myelin genes

Epigenomics ◽  
2021 ◽  
Author(s):  
Beatriz Garcia-Ruiz ◽  
Manuel Castro de Moura ◽  
Gerard Muntané ◽  
Lourdes Martorell ◽  
Elena Bosch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bipolar Disorder ◽  
Mrna Expression ◽  
Gene Expression Analysis ◽  
Mrna Levels ◽  
Healthy Controls ◽  
Genome Wide ◽  
Isoform Expression

Aim: To investigate DDR1 methylation in the brains of bipolar disorder (BD) patients and its association with DDR1 mRNA levels and comethylation with myelin genes. Materials & methods: Genome-wide profiling of DNA methylation (Infinium MethylationEPIC BeadChip) corrected for glial composition and DDR1 gene expression analysis in the occipital cortices of individuals with BD (n = 15) and healthy controls (n = 15) were conducted. Results: DDR1 5-methylcytosine levels were increased and directly associated with DDR1b mRNA expression in the brains of BD patients. We also observed that DDR1 was comethylated with a group of myelin genes. Conclusion: DDR1 is hypermethylated in BD brain tissue and is associated with isoform expression. Additionally, DDR1 comethylation with myelin genes supports the role of this receptor in myelination.

Verb paradigm in Tomo Kan Dogon: interconnections of polypredicative constructions, grammaticalization, and tonology

2021 ◽  
pp. 252-268
Author(s):  
V. V. Dyachkov ◽  
Keyword(s):  
Critical Role ◽  
The Other ◽  
Anal Ysis ◽  
Syntactic Position ◽  
The Family ◽  
Similar Range ◽  
Tonal Contour ◽  
Relationship Of

The paper deals with the grammaticalization problems in Tomo Kan (Dogon family, Niger-Congo) and, in particular, with the diachronic relationship of polypredicative constructions and TAM markers. Dogon languages are characterized by TAM systems that seem to be dia-chronically unstable since markers with a similar range of meanings go back to different lexi-cal sources in different languages of the family. TAM markers are apparently associated with polypredicative constructions, which are very common in Dogon and preserve some of their morphosyntactic properties. At the same time, Dogon languages are characterized by complex tonal changes triggered not only by phonological context but also by the syntactic position of constituents. These tonal changes, frequently referred to as tonosyntax, accompany the formation of polypredicative constructions and other syntactic phenomena. A thorough inves-tigation of Tomo Kan TAM markers shows their tonosyntactic properties to resemble those of polypredicative constructions. Moreover, assuming that tonosyntax of polypredicative con-structions triggers certain tonal contour overlays, one can account for tonal alternations ob-served in TAM forms which would have been left otherwise unexplained. However, the anal-ysis also reveals that at least two classes of TAM forms must be distinguished in Tomo Kan: one of them inherits the tonosyntax of polypredicative constructions while the other does not. A hypothesis is put forward that the latter class has a different source of grammaticalization and is probably associated with verb stem incorporation rather than with polypredication. Methodologically, the paper shows a critical role of tonology in the analysis of grammaticalization processes in tonal languages.

scholarly journals Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Aniruddha Chatterjee ◽  
Peter A. Stockwell ◽  
Euan J. Rodger ◽  
Elizabeth J. Duncan ◽  
Matthew F. Parry ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Human Neutrophils ◽  
Epigenetic Variation ◽  
Genome Wide

scholarly journals DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral modelAiptasia

2017 ◽  
Author(s):  
Yong Li ◽  
Yi Jin Liew ◽  
Guoxin Cui ◽  
Maha J Cziesielski ◽  
Noura Zahran ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Model System ◽  
Epigenetic Mechanism ◽  
Symbiotic Relationship ◽  
Epigenetic Mechanisms ◽  
Genome Wide ◽  
Spurious Transcription ◽  
Coral Reef Ecosystems

The symbiotic relationship between cnidarians and dinoflagellates is the cornerstone of coral reef ecosystems. Although research is focusing on the molecular mechanisms underlying this symbiosis, the role of epigenetic mechanisms, which have been implicated in transcriptional regulation and acclimation to environmental change, is unknown. To assess the role of DNA methylation in the cnidarian-dinoflagellate symbiosis, we analyzed genome-wide CpG methylation, histone associations, and transcriptomic states of symbiotic and aposymbiotic anemones in the model systemAiptasia. We find methylated genes are marked by histone H3K36me3 and show significant reduction of spurious transcription and transcriptional noise, revealing a role of DNA methylation in the maintenance of transcriptional homeostasis. Changes in DNA methylation and expression show enrichment for symbiosis-related processes such as immunity, apoptosis, phagocytosis recognition and phagosome formation, and unveil intricate interactions between the underlying pathways. Our results demonstrate that DNA methylation provides an epigenetic mechanism of transcriptional homeostasis during symbiosis.

scholarly journals Intergenerational epigenetic inheritance in reef-building corals

2018 ◽  
Author(s):  
Yi Jin Liew ◽  
Emily J. Howells ◽  
Xin Wang ◽  
Craig T. Michell ◽  
John A. Burt ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Intergenerational Transmission ◽  
Epigenetic Inheritance ◽  
Cpg Methylation ◽  
Epigenetic Mechanisms ◽  
Transgenerational Inheritance ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Hypermethylated Genes

MainThe notion that intergenerational or transgenerational inheritance operates solely through genetic means is slowly being eroded: epigenetic mechanisms have been shown to induce heritable changes in gene activity in plants1,2and metazoans1,3. Inheritance of DNA methylation provides a potential pathway for environmentally induced phenotypes to contribute to evolution of species and populations1–4. However, in basal metazoans, it is unknown whether inheritance of CpG methylation patterns occurs across the genome (as in plants) or as rare exceptions (as in mammals)4. Here, we demonstrate genome-wide intergenerational transmission of CpG methylation patterns from parents to sperm and larvae in a reef-building coral. We also show variation in hypermethylated genes in corals from distinct environments, indicative of responses to variations in temperature and salinity. These findings support a role of DNA methylation in the transgenerational inheritance of traits in corals, which may extend to enhancing their capacity to adapt to climate change.

scholarly journals Genome-Wide Expression of MicroRNAs Is Regulated by DNA Methylation in Hepatocarcinogenesis

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Jing Shen ◽  
Shuang Wang ◽  
Abby B. Siegel ◽  
Helen Remotti ◽  
Qiao Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Potential Role ◽  
Dna Hypermethylation ◽  
Two Phase ◽  
Genome Wide ◽  
Phase Study ◽  
A Genome ◽  
Genome Wide Expression ◽  
Inactive Chromatin

Background.Previous studies, including ours, have examined the regulation of microRNAs (miRNAs) by DNA methylation, but whether this regulation occurs at a genome-wide level in hepatocellular carcinoma (HCC) is unclear.Subjects/Methods.Using a two-phase study design, we conducted genome-wide screening for DNA methylation and miRNA expression to explore the potential role of methylation alterations in miRNAs regulation.Results.We found that expressions of 25 miRNAs were statistically significantly different between tumor and nontumor tissues and perfectly differentiated HCC tumor from nontumor. Six miRNAs were overexpressed, and 19 were repressed in tumors. Among 133 miRNAs with inverse correlations between methylation and expression, 8 miRNAs (6%) showed statistically significant differences in expression between tumor and nontumor tissues. Six miRNAs were validated in 56 additional paired HCC tissues, and significant inverse correlations were observed for miR-125b and miR-199a, which is consistent with the inactive chromatin pattern found in HepG2 cells.Conclusion.These data suggest that the expressions of miR-125b and miR-199a are dramatically regulated by DNA hypermethylation that plays a key role in hepatocarcinogenesis.

scholarly journals The Role of Stochasticity in the Origin of Epigenetic Variation in Animal Populations

2020 ◽  
Vol 60 (6) ◽  
pp. 1544-1557 ◽  
Author(s):  
C Biwer ◽  
B Kawam ◽  
V Chapelle ◽  
F Silvestre
Keyword(s):  
Dna Methylation ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Genetic Mutation ◽  
Epigenetic Variation ◽  
Epigenetic Variability ◽  
Evolutionary Potential ◽  
Environmental Variance ◽  
Animal Populations

Synopsis Epigenetic mechanisms such as DNA methylation modulate gene expression in a complex fashion are consequently recognized as among the most important contributors to phenotypic variation in natural populations of plants, animals, and microorganisms. Interactions between genetics and epigenetics are multifaceted and epigenetic variation stands at the crossroad between genetic and environmental variance, which make these mechanisms prominent in the processes of adaptive evolution. DNA methylation patterns depend on the genotype and can be reshaped by environmental conditions, while transgenerational epigenetic inheritance has been reported in various species. On the other hand, DNA methylation can influence the genetic mutation rate and directly affect the evolutionary potential of a population. The origin of epigenetic variance can be attributed to genetic, environmental, or stochastic factors. Generally less investigated than the first two components, variation lacking any predictable order is nevertheless present in natural populations and stochastic epigenetic variation, also referred to spontaneous epimutations, can sustain phenotypic diversity. Here, potential sources of such stochastic epigenetic variability in animals are explored, with a focus on DNA methylation. To this day, quantifying the importance of stochasticity in epigenetic variability remains a challenge. However, comparisons between the mutation and the epimutation rates showed a high level of the latter, suggesting a significant role of spontaneous epimutations in adaptation. The implications of stochastic epigenetic variability are multifold: by affecting development and subsequently phenotype, random changes in epigenetic marks may provide additional phenotypic diversity, which can help natural populations when facing fluctuating environments. In isogenic lineages and asexually reproducing organisms, poor or absent genetic diversity can hence be tolerated. Further implication of stochastic epigenetic variability in adaptation is found in bottlenecked invasive species populations and populations using a bet-hedging strategy.

scholarly journals The role of motivation on secondary school students’ causal attributions to choose or abandon chemistry

2020 ◽  
Author(s):  
Diego Ardura ◽  
Ángela Zamora ◽  
Alberto Pérez-Bitrián
Keyword(s):  
Secondary Education ◽  
Secondary School ◽  
Secondary School Students ◽  
Causal Attributions ◽  
The Other ◽  
Education Curriculum ◽  
School Students ◽  
The Family ◽  
The Right

The present investigation aims to analyze the effect of motivation on students’ causal attributions to choose or abandon chemistry when it first becomes optional in the secondary education curriculum in Spain. Attributions to the effect of the family and to the teacher and classroom methodology were found to be common predictors of the choice to all the students in the sample. However, our analyses point to a significant effect of the students’ motivation in other types of attributions. In the case of at-risk of abandonment students, specific causal attributions to the effect of friends and to the subject's relationship with mathematics were found. On the other hand, the effect of media was a significant predictor only in the case of highly-motivated students. Our study provides several suggestions for teachers, schools, and administrations to design counseling strategies to help students make the right choices.

scholarly journals Environmental Heterogeneity and Phenotypic Divergence: Can Heritable Epigenetic Variation Aid Speciation?

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Ruth Flatscher ◽  
Božo Frajman ◽  
Peter Schönswetter ◽  
Ovidiu Paun
Keyword(s):  
Biological Sciences ◽  
Environmental Heterogeneity ◽  
Phenotypic Diversity ◽  
Adaptive Strategies ◽  
Epigenetic Variation ◽  
Adaptive Responses ◽  
Adaptive Traits ◽  
Phenotypic Differentiation ◽  
Genome Wide

The dualism of genetic predisposition and environmental influences, their interactions, and respective roles in shaping the phenotype have been a hot topic in biological sciences for more than two centuries. Heritable epigenetic variation mediates between relatively slowly accumulating mutations in the DNA sequence and ephemeral adaptive responses to stress, thereby providing mechanisms for achieving stable, but potentially rapidly evolving phenotypic diversity as a response to environmental stimuli. This suggests that heritable epigenetic signals can play an important role in evolutionary processes, but so far this hypothesis has not been rigorously tested. A promising new area of research focuses on the interaction between the different molecular levels that produce phenotypic variation in wild, closely-related taxa that lack genome-wide genetic differentiation. By pinpointing specific adaptive traits and investigating the mechanisms responsible for phenotypic differentiation, such study systems could allow profound insights into the role of epigenetics in the evolution and stabilization of phenotypic discontinuities, and could add to our understanding of adaptive strategies to diverse environmental conditions and their dynamics.

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