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 DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 137 ◽  
Author(s):  
Shenglin Liu ◽  
Anne Aagaard ◽  
Jesper Bechsgaard ◽  
Trine Bilde
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Sequence Data ◽  
Social Spider ◽  
The Social ◽  
Genome Bisulfite Sequencing ◽  
Differential Gene ◽  
Methylation Patterns ◽  
Comparative Phylogenetic Analysis

Variation in DNA methylation patterns among genes, individuals, and populations appears to be highly variable among taxa, but our understanding of the functional significance of this variation is still incomplete. We here present the first whole genome bisulfite sequencing of a chelicerate species, the social spider Stegodyphus dumicola. We show that DNA methylation occurs mainly in CpG context and is concentrated in genes. This is a pattern also documented in other invertebrates. We present RNA sequence data to investigate the role of DNA methylation in gene regulation and show that, within individuals, methylated genes are more expressed than genes that are not methylated and that methylated genes are more stably expressed across individuals than unmethylated genes. Although no causal association is shown, this lends support for the implication of DNA CpG methylation in regulating gene expression in invertebrates. Differential DNA methylation between populations showed a small but significant correlation with differential gene expression. This is consistent with a possible role of DNA methylation in local adaptation. Based on indirect inference of the presence and pattern of DNA methylation in chelicerate species whose genomes have been sequenced, we performed a comparative phylogenetic analysis. We found strong evidence for exon DNA methylation in the horseshoe crab Limulus polyphemus and in all spider and scorpion species, while most Parasitiformes and Acariformes species seem to have lost DNA methylation.

scholarly journals Widespread natural variation of DNA methylation within angiosperms

2016 ◽  
Author(s):  
Chad E. Niederhuth ◽  
Adam J. Bewick ◽  
Lexiang Ji ◽  
Magdy S. Alabady ◽  
Kyung Do Kim ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Life Histories ◽  
Natural Variation ◽  
Gene Body ◽  
Sequencing Data ◽  
Gene Body Methylation ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data ◽  
Angiosperm Species ◽  
Methylation Patterns

AbstractTo understand the variation in genomic patterning of DNA methylation we compared methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time. These results show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

scholarly journals DNA methylome of the 20-gigabase Norway spruce genome

2016 ◽  
Vol 113 (50) ◽  
pp. E8106-E8113 ◽  
Author(s):  
Israel Ausin ◽  
Suhua Feng ◽  
Chaowei Yu ◽  
Wanlu Liu ◽  
Hsuan Yu Kuo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Somatic Embryogenesis ◽  
Norway Spruce ◽  
Biological Processes ◽  
High Coverage ◽  
Culture Cells ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing ◽  
Single Base Resolution ◽  
Methylation Patterns

DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.

scholarly journals Intergenerational transfer of DNA methylation marks in the honey bee

2020 ◽  
Vol 117 (51) ◽  
pp. 32519-32527 ◽  
Author(s):  
Boris Yagound ◽  
Emily J. Remnant ◽  
Gabriele Buchmann ◽  
Benjamin P. Oldroyd
Keyword(s):  
Dna Methylation ◽  
Honey Bee ◽  
Epigenetic Inheritance ◽  
Somatic Tissue ◽  
Methylation Profile ◽  
Evolutionary Significance ◽  
Evolutionary Potential ◽  
Mammalian Embryogenesis ◽  
Genome Bisulfite Sequencing ◽  
Methylation Patterns

The evolutionary significance of epigenetic inheritance is controversial. While epigenetic marks such as DNA methylation can affect gene function and change in response to environmental conditions, their role as carriers of heritable information is often considered anecdotal. Indeed, near-complete DNA methylation reprogramming, as occurs during mammalian embryogenesis, is a major hindrance for the transmission of nongenetic information between generations. Yet it remains unclear how general DNA methylation reprogramming is across the tree of life. Here we investigate the existence of epigenetic inheritance in the honey bee. We studied whether fathers can transfer epigenetic information to their daughters through DNA methylation. We performed instrumental inseminations of queens, each with four different males, retaining half of each male’s semen for whole genome bisulfite sequencing. We then compared the methylation profile of each father’s somatic tissue and semen with the methylation profile of his daughters. We found that DNA methylation patterns were highly conserved between tissues and generations. There was a much greater similarity of methylomes within patrilines (i.e., father-daughter subfamilies) than between patrilines in each colony. Indeed, the samples’ methylomes consistently clustered by patriline within colony. Samples from the same patriline had twice as many shared methylated sites and four times fewer differentially methylated regions compared to samples from different patrilines. Our findings indicate that there is no DNA methylation reprogramming in bees and, consequently, that DNA methylation marks are stably transferred between generations. This points to a greater evolutionary potential of the epigenome in invertebrates than there is in mammals.

scholarly journals Zbtb24 binding protects promoter activity by antagonizing DNA methylation in mESCs

2019 ◽  
Author(s):  
Haoyu Wu ◽  
David San Leon Granado ◽  
Maja Vukic ◽  
Kelly K.D. Vonk ◽  
Cor Breukel ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcriptional Activation ◽  
Zinc Finger Protein ◽  
Epigenetic Modification ◽  
Embryonic Stem ◽  
Dna Hypomethylation ◽  
Finger Protein ◽  
Genome Bisulfite Sequencing ◽  
Methylation Patterns ◽  
Unmethylated State

ABSTRACTDNA methylation is a key epigenetic modification essential for normal development. How particular factors control DNA methylation patterns and activity of a given locus is incompletely understood. The zinc finger protein Zbtb24 has been implicated in transcriptional activation/repression and the DNA methylation maintenance pathway. Here, using whole genome bisulfite sequencing in mouse embryonic stem cells, we report that besides a general trend towards DNA hypomethylation, many genomic sites gain methylation in the absence of Zbtb24 and they include promoters of actively transcribed genes. DNA hypomethylation is not generally associated with gene expression changes, suggesting that additional epigenetic safeguards are in place that ensure silencing of the affected loci. Remarkably, we identify a set of genes that is particularly susceptible to Zbtb24 occupancy. At these sites, Zbtb24 binding is not only required for gene activity but also required for maintaining the unmethylated state of the promoter.

scholarly journals Nutrition during Pregnancy Impacts Offspring's Epigenetic Status—Evidence from Human and Animal Studies

2015 ◽  
Vol 8s1 ◽  
pp. NMI.S29527 ◽  
Author(s):  
Aisling A. Geraghty ◽  
Karen L. Lindsay ◽  
Goiuri Alberdi ◽  
Fionnuala M. McAuliffe ◽  
Eileen R. Gibney
Keyword(s):  
Dna Methylation ◽  
Growth And Development ◽  
Critical Period ◽  
Animal Studies ◽  
Maternal Nutrition ◽  
Later Life ◽  
Future Health ◽  
Global Methylation ◽  
Methyl Donors ◽  
Methylation Patterns

Pregnancy is a vital time of growth and development during which maternal nutrition significantly influences the future health of both mother and baby. During pregnancy, the fetus experiences a critical period of plasticity. Epigenetics, specifically DNA methylation, plays an important role here. As nutrition is influential for DNA methylation, this review aims to determine if maternal nutrition during pregnancy can modify the offspring's epigenome at birth. Research focuses on micronutrients and methyl donors such as folate and B vitamins. Evidence suggests that maternal nutrition does not largely influence global methylation patterns, particularly in nutrient-replete populations; however, an important impact on gene-specific methylation is observed. A link is shown between maternal nutrition and the methylome of the offspring; however, there remains a paucity of research. With the potential to use DNA methylation patterns at birth to predict health of the child in later life, it is vital that further research be carried out.

scholarly journals Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation

2018 ◽  
Author(s):  
AJ Price ◽  
L Collado-Torres ◽  
NA Ivanov ◽  
W Xia ◽  
EE Burke ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Developmental Trajectories ◽  
Postnatal Life ◽  
Critical Periods ◽  
Neocortical Development ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing ◽  
Highly Correlated ◽  
Methylation Patterns

AbstractWe have characterized the landscape of DNA methylation (DNAm) across the first two decades of human neocortical development in NeuN+ neurons using whole-genome bisulfite sequencing and compared them to non-neurons (primarily glia) and prenatal homogenate cortex. We show that DNAm changes more dramatically during the first five years of postnatal life than during the entire remaining period. We further refined global patterns of increasingly divergent neuronal CpG and CpH methylation (mCpG and mCpH) into six developmental trajectories and found that in contrast to genome-wide patterns, neighboring mCpG and mCpH levels within these regions were highly correlated. We then integrated paired RNA-seq data and identified direct regulation of hundreds of transcripts and their splicing events exclusively by mCpH levels, independently from mCpG levels, across this period. We finally explored the relationship between DNAm patterns and development of brain-related phenotypes and found enriched heritability for many phenotypes within DNAm features we identify.

scholarly journals A chicken DNA methylation clock for the prediction of broiler health

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Günter Raddatz ◽  
Ryan J. Arsenault ◽  
Bridget Aylward ◽  
Rose Whelan ◽  
Florian Böhl ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Regulatory Elements ◽  
Developmental Time ◽  
Epigenetic Age ◽  
Genome Bisulfite Sequencing ◽  
Epigenetic Age Acceleration ◽  
Gene Regulatory Elements ◽  
Livestock Health ◽  
Conserved Gene ◽  
Methylation Patterns

AbstractThe domestic chicken (Gallus gallus domesticus) is the globally most important source of commercially produced meat. While genetic approaches have played an important role in the development of chicken stocks, little is known about chicken epigenetics. We have systematically analyzed the chicken DNA methylation machinery and DNA methylation landscape. While overall DNA methylation distribution was similar to mammals, sperm DNA appeared hypomethylated, which correlates with the absence of the DNMT3L cofactor in the chicken genome. Additional analysis revealed the presence of low-methylated regions, which are conserved gene regulatory elements that show tissue-specific methylation patterns. We also used whole-genome bisulfite sequencing to generate 56 single-base resolution methylomes from various tissues and developmental time points to establish an LMR-based DNA methylation clock for broiler chicken age prediction. This clock was used to demonstrate epigenetic age acceleration in animals with experimentally induced inflammation. Our study provides detailed insights into the chicken methylome and suggests a novel application of the DNA methylation clock as a marker for livestock health.

scholarly journals Prenatal Air Pollution Exposure and Placental DNA Methylation Changes: Implications on Fetal Development and Future Disease Susceptibility

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3025
Author(s):  
Terisha Ghazi ◽  
Pragalathan Naidoo ◽  
Rajen N. Naidoo ◽  
Anil A. Chuturgoon
Keyword(s):  
Heavy Metals ◽  
Dna Methylation ◽  
Air Pollution ◽  
Fetal Programming ◽  
Fetal Development ◽  
Disease Susceptibility ◽  
Current Knowledge ◽  
Later Life ◽  
In Utero ◽  
Methylation Patterns

The Developmental Origins of Health and Disease (DOHaD) concept postulates that in utero exposures influence fetal programming and health in later life. Throughout pregnancy, the placenta plays a central role in fetal programming; it regulates the in utero environment and acts as a gatekeeper for nutrient and waste exchange between the mother and the fetus. Maternal exposure to air pollution, including heavy metals, can reach the placenta, where they alter DNA methylation patterns, leading to changes in placental function and fetal reprogramming. This review explores the current knowledge on placental DNA methylation changes associated with prenatal air pollution (including heavy metals) exposure and highlights its effects on fetal development and disease susceptibility. Prenatal exposure to air pollution and heavy metals was associated with altered placental DNA methylation at the global and promoter regions of genes involved in biological processes such as energy metabolism, circadian rhythm, DNA repair, inflammation, cell differentiation, and organ development. The altered placental methylation of these genes was, in some studies, associated with adverse birth outcomes such as low birth weight, small for gestational age, and decreased head circumference. Moreover, few studies indicate that DNA methylation changes in the placenta were sex-specific, and infants born with altered placental DNA methylation patterns were predisposed to developing neurobehavioral abnormalities, cancer, and atopic dermatitis. These findings highlight the importance of more effective and stricter environmental and public health policies to reduce air pollution and protect human health.

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