scholarly journals A novel understanding of global DNA methylation in bobcat (Lynx rufus)

Genome ◽  
2020 ◽  
Vol 63 (2) ◽  
pp. 125-130
Author(s):  
Bonnie Cantrell ◽  
Sydney Friedman ◽  
Hannah Lachance ◽  
Chris Bernier ◽  
Brenda Murdoch ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Conservation Biology ◽  
Differential Methylation ◽  
Lynx Rufus ◽  
Global Dna Methylation ◽  
Epigenetic Mechanisms ◽  
Methylated Dna ◽  
Genome Wide ◽  
Weight Data ◽  
Insight Into

Epigenetic mechanisms may provide a novel prospective of bobcat (Lynx rufus) adaptation to habitat loss/fragmentation. Previous research has focused on bobcat behavior and genetics, but epigenetics has not been studied in bobcat. The aim of this study was to determine the quantity of global DNA methylation in the liver of 30 bobcats. DNA was extracted from liver samples obtained from the Vermont Fish and Wildlife Department. The percent of global DNA methylation was quantified and calculated using the MethylFlashTM Methylated DNA 5-mC Quantification Kit from Epigentek (Farmingdale, NY, USA). Age, sex, and carcass weight data were collected at sampling and analyzed with percent of global DNA methylation. Global DNA methylation was found to range from 0.46% to 2.76%. Age ranged from <1 to 12 years old and weight ranged from 3.18 to 13.61 kg. Further analysis of differential methylation may provide insight into novel means of bobcat conservation within different regions of Vermont. These results reinforce the need for genome-wide epigenetic studies in conservation biology.

Maternal intermittent fasting before mating alters hepatic DNA methylation in offspring

Epigenomics ◽  
2021 ◽  
Author(s):  
Wenzhen Yin ◽  
Yuan Liang ◽  
Lijun Sun ◽  
Yue Yin ◽  
Weizhen Zhang
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Intermittent Fasting ◽  
Global Dna Methylation ◽  
Impaired Glucose Metabolism ◽  
Methylated Dna ◽  
Glucose Levels ◽  
Blood Glucose Levels ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing

Aim: Our aim was to explore how maternal intermittent fasting (IF) influences offspring metabolism. Materials & methods: A model of female C57BL/6J mice alternate-day feeding before mating was established and alteration of hepatic DNA methylation in offspring analyzed by whole genome bisulfite sequencing. Results: IF dams weighed less (p = 0.03) and had lower random blood glucose levels (p = 0.04). Lower birth weight (p = 0.0031) and impaired glucose metabolism were also observed in the offspring of the IF mice. The hepatic genome-wide DNA methylation maps showed a correlation between maternal IF and decreased hepatic global DNA methylation of adult offspring. In the offspring liver, 2869 differentially methylated DNA regions were altered. Conclusions: Our finding suggests that maternal IF before mating significantly alters hepatic DNA methylation in offspring.

scholarly journals Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Benjamin I. Laufer ◽  
J. Antonio Gomez ◽  
Julia M. Jianu ◽  
Janine M. LaSalle
Keyword(s):  
Dna Methylation ◽  
Down Syndrome ◽  
Neuronal Differentiation ◽  
Molecular Mechanisms ◽  
Cpg Island ◽  
Differential Methylation ◽  
Chromosome 21 ◽  
Pairwise Comparisons ◽  
Genome Wide ◽  
A Genome

Abstract Background Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated). Results DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development. Conclusions Taken together, these results support a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS.

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.

Epigenetic Mechanisms in Nematode–Plant Interactions

2020 ◽  
Vol 58 (1) ◽  
pp. 119-138 ◽  
Author(s):  
Tarek Hewezi
Keyword(s):  
Dna Methylation ◽  
Effector Proteins ◽  
Plant Responses ◽  
Control Mechanisms ◽  
Epigenetic Mechanisms ◽  
Plant Interactions ◽  
Cyst Nematodes ◽  
Small Noncoding Rnas ◽  
Genome Wide ◽  
Plant Nematode

Epigenetic mechanisms play fundamental roles in regulating numerous biological processes in various developmental and environmental contexts. Three highly interconnected epigenetic control mechanisms, including small noncoding RNAs, DNA methylation, and histone modifications, contribute to the establishment of plant epigenetic profiles. During the past decade, a growing body of experimental work has revealed the intricate, diverse, and dynamic roles that epigenetic modifications play in plant–nematode interactions. In this review, I summarize recent progress regarding the functions of small RNAs in mediating plant responses to infection by cyst and root-knot nematodes, with a focus on the functions of microRNAs. I also recapitulate recent advances in genome-wide DNA methylation analysis and discuss how cyst nematodes induce extensive and dynamic changes in the plant methylome that impact the transcriptional activity of genes and transposable elements. Finally, the potential role of nematode effector proteins in triggering such epigenome changes is discussed.

scholarly journals Acetylation of UHRF1 Regulates Hemi-methylated DNA Binding and Maintenance of Genome-wide DNA Methylation

Cell Reports ◽  
2020 ◽  
Vol 32 (4) ◽  
pp. 107958
Author(s):  
Ja Young Hahm ◽  
Jin Woo Park ◽  
Joo-Young Kang ◽  
Junyoung Park ◽  
Chul-Hong Kim ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Methylated Dna ◽  
Genome Wide

scholarly journals Paternal arbuscular mycorrhizal fungal status affects DNA methylation in seeds

2017 ◽  
Vol 13 (9) ◽  
pp. 20170407 ◽  
Author(s):  
Sandra Varga ◽  
Carl D. Soulsbury
Keyword(s):  
Dna Methylation ◽  
Mycorrhizal Fungi ◽  
Seed Mass ◽  
Arbuscular Mycorrhizal ◽  
Similar Proportion ◽  
Global Dna Methylation ◽  
Transgenerational Effects ◽  
Methylated Dna ◽  
Arbuscular Mycorrhizal Fungal ◽  
First Time

Most land plants grow in association with arbuscular mycorrhizal fungi (AMF) in their roots and these fungi can cause transgenerational effects on plants' offspring. These may be caused by changes in DNA methylation of the offspring. In this study, we compared the amount of global DNA methylation in seeds of the gynodioecious plant Geranium sylvaticum in relation to the gender and the AMF status of the parents producing the seeds. The amount of DNA methylated was positively related to seed mass. Seeds produced by females had a similar proportion of methylated DNA regardless of the AMF status of the father siring the seed. By contrast, seeds from hermaphrodites had higher DNA methylation when sired by AMF fathers. We show to the best of our knowledge for the first time, that the AMF status of fathers can affect DNA methylation in seeds and that these changes in DNA methylation are further dependent on the gender of the mother producing the seeds.

scholarly journals Genome-wide DNA methylation profiles of porcine ovaries in estrus and proestrus

2018 ◽  
Vol 50 (9) ◽  
pp. 714-723 ◽  
Author(s):  
Xiaolong Zhou ◽  
Songbai Yang ◽  
Feifei Yan ◽  
Ke He ◽  
Ayong Zhao
Keyword(s):  
Dna Methylation ◽  
Epigenetic Modification ◽  
Cpg Islands ◽  
Biological Processes ◽  
Hormone Regulation ◽  
Methylated Dna ◽  
Coding Regions ◽  
Genome Wide ◽  
Differentially Methylated Genes ◽  
Flanking Regions

DNA methylation is an important epigenetic modification involved in the estrous cycle and the regulation of reproduction. Here, we investigated the genome-wide profiles of DNA methylation in porcine ovaries in proestrus and estrus using methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in intergenic and intron regions. The methylation levels of coding regions were higher than those of the 5′- and 3′-flanking regions of genes. There were 4,813 differentially methylated regions (DMRs) of CpG islands in the estrus vs. proestrus ovarian genomes. Additionally, 3,651 differentially methylated genes (DMGs) were identified in pigs in estrus and proestrus. The DMGs were significantly enriched in biological processes and pathways related to reproduction and hormone regulation. We identified 90 DMGs associated with regulating reproduction in pigs. Our findings can serve as resources for DNA methylome research focused on porcine ovaries and further our understanding of epigenetically regulated reproduction in mammals.

scholarly journals Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing

Epigenomes ◽  
2017 ◽  
Vol 1 (3) ◽  
pp. 14 ◽  
Author(s):  
Nicklas Staunstrup ◽  
Anna Starnawska ◽  
Mette Nyegaard ◽  
Anders Nielsen ◽  
Anders Børglum ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylated Dna ◽  
Genome Wide ◽  
Dna Methylation Profiling ◽  
Methylation Profiling
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