scholarly journals Alterations in epigenetic modifications during oocyte growth in mice

Reproduction ◽  
2007 ◽  
Vol 133 (1) ◽  
pp. 85-94 ◽  
Author(s):  
Shun-ichiro Kageyama ◽  
Honglin Liu ◽  
Naoto Kaneko ◽  
Masatoshi Ooga ◽  
Masao Nagata ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Epigenetic Modification ◽  
Germinal Vesicle ◽  
Epigenetic Modifications ◽  
Condensed Chromatin ◽  
Rt Pcr ◽  
Oocyte Growth ◽  
Lysine Residues ◽  
Signal Intensities

During oocyte growth, chromatin structure is altered globally and gene expression is silenced. To investigate the involvement of epigenetic modifications in the regulation of these phenomena, changes in global DNA methylation and in various histone modifications, i.e. acetylation of H3K9, H3K18, H4K5, and H4K12, and methylation of H3K4 and H3K9, were examined during the growth of mouse oocytes. Immunocytochemical analysis revealed that the signal intensities of all these modifications increased during growth and that fully grown, germinal vesicle (GV)-stage oocytes showed the most modifications. Since acetylation of most of the lysine residues on histones and methylation of H3K4 are associated with active gene expression, the increased levels of these modifications do not seem to be associated with gene silencing in GV-stage oocytes. Given that there are two types of GV-stage oocytes with different chromatin configurations and transcriptional activities, the epigenetic modification statuses of these two types were compared. The levels of all the epigenetic modifications examined were higher in the SN(surrounded nucleolus)-type oocytes, in which highly condensed chromatin is concentrated in the area around the nucleolus and gene expression is silenced than in the NSN(not surrounded nucleolus)-type oocytes, in which less-condensed chromatin does not surround the nucleolus and gene expression is active. In addition, the expression levels of various enzymes that catalyze histone modifications were shown by RT-PCR to increase with oocyte growth. Taken together, the results show that all of the epigenetic modifications increased in a concerted manner during oocyte growth, and suggest that these increases are not associated with gene expression.

scholarly journals Impact of Physical Activity and Exercise on the Epigenome in Skeletal Muscle and Effects on Systemic Metabolism

Biomedicines ◽  
2022 ◽  
Vol 10 (1) ◽  
pp. 126
Author(s):  
Julio Plaza-Diaz ◽  
David Izquierdo ◽  
Álvaro Torres-Martos ◽  
Aiman Tariq Baig ◽  
Concepción M. Aguilera ◽  
...  
Keyword(s):  
Physical Activity ◽  
Skeletal Muscle ◽  
Gene Transcription ◽  
Histone Modifications ◽  
Epigenetic Modification ◽  
Epigenetic Modifications ◽  
Late Response ◽  
Transcriptional Responses ◽  
Response To Exercise ◽  
The Impact

Exercise and physical activity induces physiological responses in organisms, and adaptations in skeletal muscle, which is beneficial for maintaining health and preventing and/or treating most chronic diseases. These adaptations are mainly instigated by transcriptional responses that ensue in reaction to each individual exercise, either resistance or endurance. Consequently, changes in key metabolic, regulatory, and myogenic genes in skeletal muscle occur as both an early and late response to exercise, and these epigenetic modifications, which are influenced by environmental and genetic factors, trigger those alterations in the transcriptional responses. DNA methylation and histone modifications are the most significant epigenetic changes described in gene transcription, linked to the skeletal muscle transcriptional response to exercise, and mediating the exercise adaptations. Nevertheless, other alterations in the epigenetics markers, such as epitranscriptomics, modifications mediated by miRNAs, and lactylation as a novel epigenetic modification, are emerging as key events for gene transcription. Here, we provide an overview and update of the impact of exercise on epigenetic modifications, including the well-described DNA methylations and histone modifications, and the emerging modifications in the skeletal muscle. In addition, we describe the effects of exercise on epigenetic markers in other metabolic tissues; also, we provide information about how systemic metabolism or its metabolites influence epigenetic modifications in the skeletal muscle.

scholarly journals Chromas from chromatin: sonification of the epigenome

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 274 ◽  
Author(s):  
Davide Cittaro ◽  
Dejan Lazarevic ◽  
Paolo Provero
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Functional Properties ◽  
Histone Modifications ◽  
Epigenetic Modifications ◽  
Phenotypic Properties ◽  
Multiple Signals ◽  
Meaningful Information ◽  
Musical Scores ◽  
Differential Gene

The epigenetic modifications are organized in patterns determining the functional properties of the underlying genome. Such patterns, typically measured by ChIP-seq assays of histone modifications, can be combined and translated into musical scores, summarizing multiple signals into a single waveform. As music is recognized as a universal way to convey meaningful information, we wanted to investigate properties of music obtained by sonification of ChIP-seq data. We show that the music produced by such quantitative signals is perceived by human listeners as more pleasant than that produced from randomized signals. Moreover, the waveform can be analyzed to predict phenotypic properties, such as differential gene expression.

scholarly journals No effect of acute exercise on the dynamic change in the expression of genes involved in epigenetic modification in professional athletes

2021 ◽  
Author(s):  
Witold Józef Światowy ◽  
Jacek Zieliński ◽  
Maria Aleksandra Osielska ◽  
Krzysztof Kusy ◽  
Dariusz Wieliński ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Exercise ◽  
Epigenetic Modification ◽  
Dynamic Change ◽  
Epigenetic Modifications ◽  
Professional Athletes ◽  
Peak Exercise ◽  
Gene Transcript ◽  
Interesting Phenomenon ◽  
Expression Of Genes

Abstract Background:The adaptation of the organism to exercise in the context of gene expression profile is an interesting phenomenon. Exercise can change the expression of individual genes due to changes in the degree of DNA methylation, changes in miRNA expression, or through methylation or acetylation of histones.Hypothesis:Acute exercise increases the expression of genes such as HDAC1, DNMT1, and JHDM1D that can affect epigenetic modifications in PBMCs.Methods:The aim of this study was to determine whether there was a change in gene expression in the blood cells during acute exercise and after a 1-hour recovery. The transcriptions of genes involved in epigenetic modifications (HDAC1, HDAC1 and JHDM1D) were examined in 9 professional athletes at rest, during consecutive stages of a treadmill exercise until exhaustion, and following recovery.Results:No significant differences in the level of transcript were observed in the course of the experiment in the tested PBMC cells. On the other hand, a significant (p = 0.007) correlation was observed in the level of the JHDM1D gene transcript and the number of monocytes in the samples obtained after reaching peak exercise intensity, but in the initial samples this correlation was not significant (p = 0.053).Conclusion:Acute physical exercise does not rapidly alter the transcript levels of the JHDM1D, DNMT1 and HDAC1 genes in PBMCs. The observed correlation between the level of JHDM1D mRNA and the level of monocytes and HDAC1 with lymphocytes requires further investigation.

scholarly journals Slowing Down Ageing: The Role of Nutrients and Microbiota in Modulation of the Epigenome

Nutrients ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1251 ◽  
Author(s):  
Agnieszka Gadecka ◽  
Anna Bielak-Zmijewska
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Structural Changes ◽  
Epigenetic Modification ◽  
Condensed Chromatin ◽  
Gene Promoters ◽  
Methylation Of Dna ◽  
Age Related ◽  
Altered Gene

The human population is getting ageing. Both ageing and age-related diseases are correlated with an increased number of senescent cells in the organism. Senescent cells do not divide but are metabolically active and influence their environment by secreting many proteins due to a phenomenon known as senescence associated secretory phenotype (SASP). Senescent cells differ from young cells by several features. They possess more damaged DNA, more impaired mitochondria and an increased level of free radicals that cause the oxidation of macromolecules. However, not only biochemical and structural changes are related to senescence. Senescent cells have an altered chromatin structure, and in consequence, altered gene expression. With age, the level of heterochromatin decreases, and less condensed chromatin is more prone to DNA damage. On the one hand, some gene promoters are easily available for the transcriptional machinery; on the other hand, some genes are more protected (locally increased level of heterochromatin). The structure of chromatin is precisely regulated by the epigenetic modification of DNA and posttranslational modification of histones. The methylation of DNA inhibits transcription, histone methylation mostly leads to a more condensed chromatin structure (with some exceptions) and acetylation plays an opposing role. The modification of both DNA and histones is regulated by factors present in the diet. This means that compounds contained in daily food can alter gene expression and protect cells from senescence, and therefore protect the organism from ageing. An opinion prevailed for some time that compounds from the diet do not act through direct regulation of the processes in the organism but through modification of the physiology of the microbiome. In this review we try to explain the role of some food compounds, which by acting on the epigenetic level might protect the organism from age-related diseases and slow down ageing. We also try to shed some light on the role of microbiome in this process.

scholarly journals Role of Tet2 in Regulating Adaptive and Innate Immunity

2021 ◽  
Vol 9 ◽  
Author(s):  
Jiaqi Li ◽  
Lifang Li ◽  
Xiaoxiao Sun ◽  
Tuo Deng ◽  
Gan Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Targets ◽  
Gene Expression Regulation ◽  
Epigenetic Modification ◽  
Epigenetic Modifications ◽  
Cellular Factors ◽  
Tet Enzymes ◽  
And Function ◽  
Opposing Effects ◽  
Tet Protein

Accumulated evidence indicates that epigenetic modifications play central roles in gene expression regulation and participate in developing many autoimmune and autoinflammatory diseases. Mechanistically, epigenetic modifications act as a bridge between environmental and cellular factors and susceptibility genes. DNA methylation is a critical epigenetic modification that is regulated by ten-eleven translocation (TET) enzymes. Accumulating evidence has revealed that TET family proteins function as gene regulators and antitumor drug targets mainly because of their ability to oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Recently, the effect of Tet2, an essential TET protein, on the development of autoimmune diseases has been explored. In this review, we summarize the current understanding of Tet2 in immune response regulation, clarify the mechanisms of Tet2 in B and T cell differentiation and function, and discuss the opposing effects of Tet2 on inflammatory gene expression in the immune system to provide new potential therapeutic targets for related diseases.

scholarly journals Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e5840 ◽  
Author(s):  
Jeongwoo Kwon ◽  
Ying-Hua Li ◽  
Yu-Jin Jo ◽  
YoungJin Oh ◽  
Suk Namgoong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Glycogen Synthase ◽  
Epigenetic Modification ◽  
Mammalian Species ◽  
Embryonic Stem ◽  
Cell Number ◽  
Epigenetic Modifications ◽  
Related Gene ◽  
Developmental Potential ◽  
Blastocyst Quality

Inhibition of both MEK1/2 and glycogen synthase kinase-3 (GSK3; 2i system) facilitates the maintenance of naïve stemness for embryonic stem cells in various mammalian species. However, the effect of the inhibition of the 2i system on porcine early embryogenesis is unknown. We investigated the effect of the 2i system on early embryo development, expression of pluripotency-related genes, and epigenetic modifications. Inhibition of MEK1/2 (by PD0325901) and/or GSK3 (by CHIR99021) did not alter the developmental potential of porcine parthenogenetic embryos, but improved blastocyst quality, as judged by the blastocyst cell number, diameter, and reduction in the number of apoptotic cells. The expression levels of octamer-binding transcription factor 4 and SOX2, the primary transcription factors that maintain embryonic pluripotency, were significantly increased by 2i treatments. Epigenetic modification-related gene expression was altered upon 2i treatment. The collective results indicate that the 2i system in porcine embryos improved embryo developmental potential and blastocyst quality by regulating epigenetic modifications and pluripotency-related gene expression.

scholarly journals Epigenetics and sarcoidosis

2021 ◽  
Vol 30 (160) ◽  
pp. 210076
Author(s):  
Iain R. Konigsberg ◽  
Lisa A. Maier ◽  
Ivana V. Yang
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Lung Disease ◽  
Histone Modifications ◽  
Genetic Variants ◽  
Lung Diseases ◽  
Hypersensitivity Pneumonitis ◽  
Epigenetic Modifications ◽  
Regulatory Mechanisms ◽  
Beryllium Disease

Epigenetic modifications are emerging as important regulatory mechanisms of gene expression in lung disease, given that they are influenced by environmental exposures and genetic variants, and that they regulate immune and fibrotic processes. In this review, we introduce these concepts with a focus on the study of DNA methylation and histone modifications and discuss how they have been applied to lung disease, and how they can be applied to sarcoidosis. This information has implications for other exposure and immunologically mediated lung diseases, such as chronic beryllium disease, hypersensitivity pneumonitis, and asbestosis.

scholarly journals Epigenetic evidence of an Ac/Dc axis by VPA and SAHA

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Sebastian Lunke ◽  
Scott Maxwell ◽  
Ishant Khurana ◽  
Harikrishnan K.N. ◽  
Jun Okabe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Acetylation ◽  
Histone Modifications ◽  
Target Genes ◽  
Hdac Inhibitors ◽  
Histone Deacetylation ◽  
Lysine Methylation ◽  
Blocking Voltage ◽  
Lysine Residues ◽  
Voltage Gated Ion Channels

Abstract Background Valproic acid (VPA) is one of the most commonly used anti-epileptic drugs with pharmacological actions on GABA and blocking voltage-gated ion channels. VPA also inhibits histone deacetylase (HDAC) activity. Suberoylanilide hydroxamic acid is also a member of a larger class of compounds that inhibit HDACs. At the time of this article, there are 123 active international clinical trials for VPA (also known as valproate, convulex, divalproex, and depakote) and SAHA (vorinostat, zolinza). While it is well known that VPA and SAHA influence the accumulation of acetylated lysine residues on histones, their true epigenetic complexity remains poorly understood. Results Primary human cells were exposed to VPA and SAHA to understand the extent of histone acetylation (H3K9/14ac) using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Because histone acetylation is often associated with modification of lysine methylation, we also examined H3K4me3 and H3K9me3. To assess the influence of the HDAC inhibitors on gene expression, we used RNA sequencing (RNA-seq). ChIP-seq reveals a distribution of histone modifications that is robust and more broadly regulated than previously anticipated by VPA and SAHA. Histone acetylation is a characteristic of the pharmacological inhibitors that influenced gene expression. Surprisingly, we observed histone deacetylation by VPA stimulation is a predominant signature following SAHA exposure and thus defines an acetylation/deacetylation (Ac/Dc) axis. ChIP-seq reveals regionalisation of histone acetylation by VPA and broader deacetylation by SAHA. Independent experiments confirm H3K9/14 deacetylation of NFκB target genes by SAHA. Conclusions The results provide an important framework for understanding the Ac/Dc axis by highlighting a broader complexity of histone modifications by the most established and efficacious anti-epileptic medication in this class, VPA and comparison with the broad spectrum HDAC inhibitor, SAHA.

scholarly journals Out of sight, out of mind? Germ cells and the potential impacts of epigenomic drugs

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1967 ◽  
Author(s):  
Ellen G. Jarred ◽  
Heidi Bildsoe ◽  
Patrick S. Western
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Modifications ◽  
Germ Cells ◽  
Epigenetic Modifications ◽  
Reproductive Age ◽  
Specific Gene ◽  
And Function ◽  
Substantial Interest ◽  
Target Effects

Epigenetic modifications, including DNA methylation and histone modifications, determine the way DNA is packaged within the nucleus and regulate cell-specific gene expression. The heritability of these modifications provides a memory of cell identity and function. Common dysregulation of epigenetic modifications in cancer has driven substantial interest in the development of epigenetic modifying drugs. Although these drugs have the potential to be highly beneficial for patients, they act systemically and may have “off-target” effects in other cells such as the patients’ sperm or eggs. This review discusses the potential for epigenomic drugs to impact on the germline epigenome and subsequent offspring and aims to foster further examination into the possible effects of these drugs on gametes. Ultimately, the information gained by further research may improve the clinical guidelines for the use of such drugs in patients of reproductive age.

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