scholarly journals Regional epigenetic variation in asexual snail populations among urban and rural lakes

2019 ◽  
Vol 5 (4) ◽  
Author(s):  
Jennifer L M Thorson ◽  
Mark Smithson ◽  
Ingrid Sadler-Riggleman ◽  
Daniel Beck ◽  
Mark Dybdahl ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Environmental Factors ◽  
Geographic Distance ◽  
Dispersal Distance ◽  
Population History ◽  
Northwest Pacific ◽  
Sample Population ◽  
Epigenetic Variation ◽  
Urban Lake ◽  
Urban Lakes

Abstract Epigenetic variation has the potential to influence environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the capacity to respond through epigenetic variation. An epigenetic response could be even more important in a population when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. Snails were collected from a more pristine rural Lake 1 (Lake Lytle), and two urban lakes, Lake 2 (Capitol Lake) and Lake 3 (Lake Washington) on the Northwest Pacific coast. DNA methylation was assessed for each sample population using methylated DNA immunoprecipitation, MeDIP, followed by next-generation sequencing. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2, and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. The presence of site-specific differences between each of these lake populations suggest an epigenetic response to varied environmental factors. The results do not support an effect of geographic distance in these populations. The role of dispersal distance among lakes, population history, environmental pollution and stably inherited methylation versus environmentally triggered methylation in producing the observed epigenetic variation are discussed. Observations support the proposal that epigenetic alterations may associate with phenotypic variation and environmental factors and history of the different lakes.

scholarly journals Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 291
Author(s):  
Biao Ni ◽  
Jian You ◽  
Jiangnan Li ◽  
Yingda Du ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Soil Properties ◽  
Changbai Mountains ◽  
Epigenetic Variation ◽  
Geographical Distance ◽  
Mantel Tests ◽  
Epigenetic Diversity ◽  
Different Populations

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

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

DNA methylation in human sperm: a systematic review

2020 ◽  
Vol 26 (6) ◽  
pp. 841-873 ◽  
Author(s):  
Fredrika Åsenius ◽  
Amy F Danson ◽  
Sarah J Marzi
Keyword(s):  
Systematic Review ◽  
Dna Methylation ◽  
Environmental Factors ◽  
Pregnancy Outcomes ◽  
Human Sperm ◽  
Semen Parameters ◽  
Dna Methylome ◽  
Sperm Dna ◽  
Offspring Health

Abstract BACKGROUND Studies in non-human mammals suggest that environmental factors can influence spermatozoal DNA methylation, and some research suggests that spermatozoal DNA methylation is also implicated in conditions such as subfertility and imprinting disorders in the offspring. Together with an increased availability of cost-effective methods of interrogating DNA methylation, this premise has led to an increasing number of studies investigating the DNA methylation landscape of human spermatozoa. However, how the human spermatozoal DNA methylome is influenced by environmental factors is still unclear, as is the role of human spermatozoal DNA methylation in subfertility and in influencing offspring health. OBJECTIVE AND RATIONALE The aim of this systematic review was to critically appraise the quality of the current body of literature on DNA methylation in human spermatozoa, summarize current knowledge and generate recommendations for future research. SEARCH METHODS A comprehensive literature search of the PubMed, Web of Science and Cochrane Library databases was conducted using the search terms ‘semen’ OR ‘sperm’ AND ‘DNA methylation’. Publications from 1 January 2003 to 2 March 2020 that studied human sperm and were written in English were included. Studies that used sperm DNA methylation to develop methodologies or forensically identify semen were excluded, as were reviews, commentaries, meta-analyses or editorial texts. The Grading of Recommendations, Assessment, Development and Evaluations (GRADE) criteria were used to objectively evaluate quality of evidence in each included publication. OUTCOMES The search identified 446 records, of which 135 were included in the systematic review. These 135 studies were divided into three groups according to area of research; 56 studies investigated the influence of spermatozoal DNA methylation on male fertility and abnormal semen parameters, 20 studies investigated spermatozoal DNA methylation in pregnancy outcomes including offspring health and 59 studies assessed the influence of environmental factors on spermatozoal DNA methylation. Findings from studies that scored as ‘high’ and ‘moderate’ quality of evidence according to GRADE criteria were summarized. We found that male subfertility and abnormal semen parameters, in particular oligozoospermia, appear to be associated with abnormal spermatozoal DNA methylation of imprinted regions. However, no specific DNA methylation signature of either subfertility or abnormal semen parameters has been convincingly replicated in genome-scale, unbiased analyses. Furthermore, although findings require independent replication, current evidence suggests that the spermatozoal DNA methylome is influenced by cigarette smoking, advanced age and environmental pollutants. Importantly however, from a clinical point of view, there is no convincing evidence that changes in spermatozoal DNA methylation influence pregnancy outcomes or offspring health. WIDER IMPLICATIONS Although it appears that the human sperm DNA methylome can be influenced by certain environmental and physiological traits, no findings have been robustly replicated between studies. We have generated a set of recommendations that would enhance the reliability and robustness of findings of future analyses of the human sperm methylome. Such studies will likely require multicentre collaborations to reach appropriate sample sizes, and should incorporate phenotype data in more complex statistical models.

scholarly journals : Seasonal zooplankton dynamics and its relations with environmental factors in Dalcar Urban Lake (Córdoba, Argentina)

2018 ◽  
Vol 20 ◽  
pp. 297-309
Author(s):  
Alicia Vignatti ◽  
Santiago Echaniz ◽  
Gabriela Cabrera ◽  
Miguel Mancini ◽  
Victor Salinas
Keyword(s):  
Environmental Factors ◽  
Urban Lake ◽  
Zooplankton Dynamics

scholarly journals Disentangling age-dependent DNA methylation: deterministic, stochastic, and nonlinear

2020 ◽  
Author(s):  
O. Vershinina ◽  
M. Ivanchenko ◽  
M.G. Bacalini ◽  
A. Zaikin ◽  
C. Franceschi
Keyword(s):  
Dna Methylation ◽  
Environmental Factors ◽  
Methylation Level ◽  
Signal To Noise Ratio ◽  
Cross Sectional ◽  
Ample Evidence ◽  
Systematic Assessment ◽  
Relative Contribution ◽  
Age Dependent ◽  
The Individual

ABSTRACTDNA methylation variability arises due to concurrent genetic and environmental influences. Each of them is a mixture of regular and noisy sources, whose relative contribution has not been satisfactorily understood yet. We conduct a systematic assessment of the age-dependent methylation by the signal-to-noise ratio and identify a wealth of “deterministic” CpG probes (about 90%), whose methylation variability likely originates due to genetic and general environmental factors. The remaining 10% of “stochastic” CpG probes are arguably governed by the biological noise or incidental environmental factors. Investigating the mathematical functional relationship between methylation levels and variability, we find that in about 90% of the age-associated differentially methylated positions, the variability changes as the square of the methylation level, whereas in the most of the remaining cases the dependence is linear. Furthermore, we demonstrate that the methylation level itself in more than 15% cases varies nonlinearly with age (according to the power law), in contrast to the previously assumed linear changes. Our findings present ample evidence of the ubiquity of strong DNA methylation regulation, resulting in the individual age-dependent and nonlinear methylation trajectories, whose divergence explains the cross-sectional variability. It may also serve a basis for constructing novel nonlinear epigenetic clocks.

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 Health Evaluation and Risk Factor Identification of Urban Lakes—A Case Study of Lianshi Lake

Water ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1428
Author(s):  
Wei Su ◽  
Jiapeng Wu ◽  
Bei Zhu ◽  
Kaiqi Chen ◽  
Wenqi Peng ◽  
...  
Keyword(s):  
Risk Factors ◽  
Risk Factor ◽  
Ecological Restoration ◽  
Landscape Connectivity ◽  
Hydrodynamic Characteristics ◽  
Scientific Management ◽  
Lake Ecosystem ◽  
Health Evaluation ◽  
Urban Lake ◽  
Urban Lakes

Health assessment and risk factor identification represent the premise and foundation of scientific management and ecological restoration of urban lakes. Based on in-depth understanding of the nature–society duality of urban lakes, a framework for evaluating urban lake health was constructed, including four modules, namely, establishing an index system; determining the index weight; identifying risk factors; and a comprehensive lake health evaluation. Employing this framework, we evaluated Lianshi Lake, Beijing, classifying the lake condition as “sub-healthy”. Based on the evaluation data, we identified the health risk factors of the lake. We applied standard difference rate (SDR) and risk degree (Rd) (safe degree (Sd)) concepts, and classified the indices of risk areas employing the Pareto analysis method. Finally, we identified the lake residence period, landscape connectivity, and eutrophication as the major risk factors in Lianshi Lake. Three factors constitute the basis of ecosystem health and are key targets of ecological restoration: the lake residence period represents the hydrological and hydrodynamic characteristics of the lake; landscape connectivity is described from an ecological perspective, and represents the integrity of the lake ecosystem; and the eutrophication states describe the water quality characteristics and represent the availability of lake water. The results contribute to decision-making for comprehensive urban lake management.

scholarly journals Epigenetic Variation Analysis Leads to Biomarker Discovery in Gastric Adenocarcinoma

2020 ◽  
Vol 11 ◽  
Author(s):  
Yan Zhang ◽  
Dianjing Guo
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Dna Methylation ◽  
Gastric Adenocarcinoma ◽  
Histone Modifications ◽  
Biomarker Discovery ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Integrated Analysis ◽  
Epigenetic Variation

As one of the most common malignant tumors worldwide, gastric adenocarcinoma (GC) and its prognosis are still poorly understood. Various genetic and epigenetic factors have been indicated in GC carcinogenesis. However, a comprehensive and in-depth investigation of epigenetic alteration in gastric cancer is still missing. In this study, we systematically investigated some key epigenetic features in GC, including DNA methylation and five core histone modifications. Data from The Cancer Genome Atlas Program and other studies (Gene Expression Omnibus) were collected, analyzed, and validated with multivariate statistical analysis methods. The landscape of epi-modifications in gastric cancer was described. Chromatin state transition analysis showed a histone marker shift in gastric cancer genome by employing a Hidden-Markov-Model based approach, indicated that histone marks tend to label different sets of genes in GC compared to control. An additive effect of these epigenetic marks was observed by integrated analysis with gene expression data, suggesting epigenetic modifications may cooperatively regulate gene expression. However, the effect of DNA methylation was found more significant without the presence of the five histone modifications in our study. By constructing a PPI network, key genes to distinguish GC from normal samples were identified, and distinct patterns of oncogenic pathways in GC were revealed. Some of these genes can also serve as potential biomarkers to classify various GC molecular subtypes. Our results provide important insights into the epigenetic regulation in gastric cancer and other cancers in general. This study describes the aberrant epigenetic variation pattern in GC and provides potential direction for epigenetic biomarker discovery.

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