scholarly journals DNA methylation modification is associated with gonadal differentiation in Monopterus albus

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xin Wang ◽  
Fengling Lai ◽  
Jun Xiong ◽  
Wang Zhu ◽  
Bifeng Yuan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Epigenetic Modification ◽  
Dynamic Change ◽  
Regulation Mechanism ◽  
Gonadal Differentiation ◽  
Monopterus Albus ◽  
Hormone Synthesis ◽  
Expression Site ◽  
Cytochrome P450 Family

Abstract Background Both testis and ovary can be produced sequentially in an individual with the same genome when sex reversal occurs in the teleost Monopterus albus, and epigenetic modification is supposed to be involved in gonadal differentiation. However, DNA methylation regulation mechanism underlying the gonadal differentiation remains unclear. Results Here, we used liquid chromatography-electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS) to simultaneously determine endogenous levels of both 5-methyl-2′-deoxycytidine (m5dC) and 5-hydroxymethyl-2′-deoxycytidine (hm5dC) during gonadal differentiation. Overall DNA methylation level was upregulated from ovary to testis via ovotestis. As a de novo methylase, dnmt3aa expression was also upregulated in the process. Notably, we determined transcription factor Foxa1 for dnmt3aa gene expression. Site-specific mutations and chromatin immunoprecipitation showed that Foxa1 can bind to and activate the dnmt3aa promoter. Furthermore, DNA methylation levels of key genes foxl2 (forkhead box L2) and cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a) in regulation of female hormone synthesis were consistently upregulated during gonadal differentiation. Conclusions These data suggested that dynamic change of DNA methylation modification is associated with gonadal differentiation.

scholarly journals Analysis of genomic DNA methylation and gene transcription modulation induced by DNMT3A deficiency in HEK293 cells

2020 ◽  
Author(s):  
Mengxiao Zhang ◽  
Jiaxian Wang ◽  
Qiuxiang Tian ◽  
Lei Feng ◽  
Hui Yang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Growth ◽  
Transcriptional Repression ◽  
Catalytic Domain ◽  
De Novo ◽  
Epigenetic Modification ◽  
Cell Metabolism ◽  
Dna Methyltransferases ◽  
Hek293 Cells ◽  
Signal Pathways

AbstractDNA methylation is an important epigenetic modification associated with transcriptional repression, and plays key roles in normal cell growth as well as oncogenesis. Among the three main DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B), DNMT3A mediates de novo DNA methylation with partial functional redundancy with DNMT3B. However, the general effects of DNMT3A and its downstream gene regulation profile are yet to be unveiled. In the present study, we used CRISPR/Cas9 technology to successfully create DNMT3A deficient human embryonic kidney cell line HEK293, with frameshift mutations in its catalytic domain. Our results showed that the cell growth slowed down in DNMT3A knockout cells. UPLC-MS analysis of DNMT3A deficient cells showed that the genome-level DNA methylation was reduced by 21.5% and led to an impairment of cell proliferation as well as a blockage of MAPK and PI3K-Akt pathways. Whole genome RNA-seq revealed that DNMT3A knockout up-regulated expression of genes and pathways related to cell metabolism but down-regulated those involved in ribosome function, which explained the inhibition of cell growth and related signal pathways. Further, bisulfite DNA treatment showed that DNMT3A ablation reduced the methylation level of DNMT3B gene as well, indicating the higher DNMT3B activity and thereby explaining those down-regulated profiles of genes.

scholarly journals Epigenetic Modification Is Regulated by the Interaction of Influenza A Virus Nonstructural Protein 1 with the De Novo DNA Methyltransferase DNMT3B and Subsequent Transport to the Cytoplasm for K48-Linked Polyubiquitination

2019 ◽  
Vol 93 (7) ◽  
Author(s):  
Shi Liu ◽  
Li Liu ◽  
Gang Xu ◽  
Zhongying Cao ◽  
Qing Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Influenza A Virus ◽  
Influenza A ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Epigenetic Modification ◽  
Nonstructural Protein ◽  
Ns1 Protein ◽  
Nonstructural Protein 1 ◽  
Stat Signaling

ABSTRACT The influenza virus nonstructural protein 1 (NS1) is a nonstructural protein that plays a major role in antagonizing host interferon responses during infection. However, a clear role for the NS1 protein in epigenetic modification has not been established. In this study, NS1 was found to regulate the expression of some key regulators of JAK-STAT signaling by inhibiting the DNA methylation of their promoters. Furthermore, DNA methyltransferase 3B (DNMT3B) is responsible for this process. Upon investigating the mechanisms underlying this event, NS1 was found to interact with DNMT3B but not DNMT3A, leading to the dissociation of DNMT3B from the promoters of the corresponding genes. In addition, the interaction between NS1 and DNMT3B changed the localization of DNMT3B from the nucleus to the cytosol, resulting in K48-linked ubiquitination and degradation of DNMT3B in the cytosol. We conclude that NS1 interacts with DNMT3B and changes its localization to mediate K48-linked polyubiquitination, subsequently contributing to the modulation of the expression of JAK-STAT signaling suppressors. IMPORTANCE The nonstructural protein 1 (NS1) of the influenza A virus (IAV) is a multifunctional protein that counters cellular antiviral activities and is a virulence factor. However, the involvement of NS1 in DNA methylation during IAV infection has not been established. Here, we reveal that the NS1 protein binds the cellular DNMT3B DNA methyltransferase, thereby inhibiting the methylation of the promoters of genes encoding suppressors of JAK-STAT signaling. As a result, these suppressor genes are induced, and JAK-STAT signaling is inhibited. Furthermore, we demonstrate that the NS1 protein transports DNMT3B to the cytoplasm for ubiquitination and degradation. Thus, we identify the NS1 protein as a potential trigger of the epigenetic deregulation of JAK-STAT signaling suppressors and illustrate a novel mechanism underlying the regulation of host immunity during IAV infection.

scholarly journals Genome wide efficiency profiling reveals modulation of maintenance and de novo methylation by Tets

2020 ◽  
Author(s):  
Pascal Giehr ◽  
Charalampos Kyriakopoulos ◽  
Karl Nordström ◽  
Abduhlrahman Salhab ◽  
Fabian Müller ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Epigenetic Modification ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Sequencing Data ◽  
Reduced Representation ◽  
Genome Wide ◽  
Global And Local

AbstractBackgroundDNA methylation is an essential epigenetic modification which is set and maintained by DNA methyl transferases (Dnmts) and removed via active and passive mechanisms involving Tet mediated oxidation. While the molecular mechanisms of these enzymes are well studied, their interplay on shaping cell specific methylomes remains less well understood. In our work we model the activities of Tets and Dnmts at single CpGs across the genome using a novel type of high resolution sequencing data.ResultsTo accurately measure 5mC and 5hmC levels at single CpGs we developed RRHPoxBS, a reduced representation hairpin oxidative bisulfite sequencing approach. Using this method we mapped the methylomes and hydroxymethylomes of wild type and Tet triple knockout mouse embryonic stem cells. These comprehensive datasets were then used to develop an extended Hidden Markov model allowing us i) to determine the symmetrical methylation and hydroxymethylation state at millions of individual CpGs, ii) infer the maintenance and de novo methylation efficiencies of Dnmts and the hydroxylation efficiencies of Tets at individual CpG positions. We find that Tets exhibit their highest activity around unmethylated regulatory elements, i.e. active promoters and enhancers. Furthermore, we find that Tets’ presence has a profound effect on the global and local maintenance and de novo methylation activities by the Dnmts, not only substantially contributing to a universal demethylation of the genome but also shaping the overall methylation landscape.ConclusionsOur analysis demonstrates that a fine tuned and locally controlled interplay between Tets and Dnmts is important to modulate de novo and maintenance activities of Dnmts across the genome. Tet activities contribute to DNA methylation patterning in the following ways: They oxidize 5mC, they locally shield DNA from accidental de novo methylation and at the same time modulate maintenance and de novo methylation efficiencies of Dnmts across the genome.

scholarly journals DNA Methylation Events as Markers for Diagnosis and Management of Acute Myeloid Leukemia and Myelodysplastic Syndrome

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Geórgia Muccillo Dexheimer ◽  
Jayse Alves ◽  
Laura Reckziegel ◽  
Gabrielle Lazzaretti ◽  
Ana Lucia Abujamra
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukemia ◽  
Myelodysplastic Syndrome ◽  
Myeloid Leukemia ◽  
Epigenetic Modification ◽  
Dynamic Change ◽  
Cellular Transformation ◽  
Response To Therapy ◽  
Response To Treatment ◽  
Acute Myeloid

During the onset and progression of hematological malignancies, many changes occur in cellular epigenome, such as hypo- or hypermethylation of CpG islands in promoter regions. DNA methylation is an epigenetic modification that regulates gene expression and is a key event for tumorigenesis. The continuous search for biomarkers that signal early disease, indicate prognosis, and act as therapeutic targets has led to studies investigating the role of DNA in cancer onset and progression. This review focuses on DNA methylation changes as potential biomarkers for diagnosis, prognosis, response to treatment, and early toxicity in acute myeloid leukemia and myelodysplastic syndrome. Here, we report that distinct changes in DNA methylation may alter gene function and drive malignant cellular transformation during several stages of leukemogenesis. Most of these modifications occur at an early stage of disease and may predict myeloid/lymphoid transformation or response to therapy, which justifies its use as a biomarker for disease onset and progression. Methylation patterns, or its dynamic change during treatment, may also be used as markers for patient stratification, disease prognosis, and response to treatment. Further investigations of methylation modifications as therapeutic biomarkers, which may correlate with therapeutic response and/or predict treatment toxicity, are still warranted.

scholarly journals Analysis of Genomic DNA Methylation and Gene Transcription Modulation Induced by DNMT3A Deficiency in HEK293 Cells

2020 ◽  
Author(s):  
Mengxiao Zhang ◽  
Jiaxian Wang ◽  
Qiuxiang Tian ◽  
Lei Feng ◽  
Hui Yang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Growth ◽  
Transcriptional Repression ◽  
Genomic Dna ◽  
Catalytic Domain ◽  
De Novo ◽  
Epigenetic Modification ◽  
Dna Methyltransferases ◽  
Hek293 Cells ◽  
Signal Pathways

Abstract Background DNA methylation is an important epigenetic modification associated with transcriptional repression, and plays key roles in normal cell growth as well as oncogenesis. Among the three main DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B), DNMT3A mediates de novo DNA methylation with partial functional redundancy with DNMT3B. However, the general effects of DNMT3A and its downstream gene regulation profile are yet to be unveiled. Results In the present study, we used CRISPR/Cas9 technology to successfully create DNMT3A deficient human embryonic kidney cell line HEK293, with frameshift mutations in its catalytic domain. Our results showed that the cell growth slowed down in DNMT3A knockout cells. UPLC-MS analysis of DNMT3A deficient cells showed that the genome-level DNA methylation was reduced by 21.5% and led to an impairment of cell proliferation as well as a blockage of MAPK and PI3K-Akt pathways. Whole genome RNA-seq revealed that DNMT3A knockout up-regulated expression of genes and pathways related to cell metabolism but down-regulated those involved in ribosome function, which explained the inhibition of cell growth and related signal pathways. Further, bisulfite DNA treatment showed that DNMT3A ablation reduced the methylation level of DNMT3B gene as well, indicating the higher DNMT3B activity and thereby explaining those down-regulated profiles of genes.Conclusions Our work is the first report on the effect of DNMT3A disruption in its catalytic domain, demonstrating that DNMT3A plays a key role on genomic DNA methylation and expression, and suggesting that DNMT3A could be an ideal target for the development of personalized treatment or to predict tumor prognosis.

scholarly journals DNA Epigenome Editing Using Crispr-Cas Suntag-Directed DNMT3A

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2707-2707 ◽  
Author(s):  
Yung-Hsin Huang ◽  
Su Jianzhong ◽  
Yong Lei ◽  
Michael C Gundry ◽  
Xiaotian Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
De Novo ◽  
Conflicts Of Interest ◽  
Epigenetic Modification ◽  
Poor Correlation ◽  
Reduced Representation ◽  
Peptide Epitopes ◽  
Epigenome Editing ◽  
Multiple Copies

Abstract DNA methylation, an epigenetic modification, has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global patterns of DNA methylation and gene expression. To overcome this barrier, we utilized nuclease-deactivated Cas9 protein fused to repetitive peptide epitopes (SunTag) recruiting multiple copies of antibody-fused de novo DNA methyltranferase 3A (DNMT3A) (CRISPR-Cas SunTag-directed DNMT3A) to amplify local DNMT3A concentration and to methylate genomic sites of interest. Here, we demonstrated that CRISPR-Cas SunTag-directed DNMT3A not only dramatically increased CpG methylation but also, to our surprise, CpH (H =A or C or T) methylation at the HOXA5 lociin human embryonic kidney 293T cells (HEK293T). Furthermore, using a single sgRNA, CRISPR-Cas SunTag-directed DNMT3A was capable of methylating 4.5 kb genomic regions, surpassing previous targeted methylation tools whose activity is limited to 200bp. Using reduced representation bisulfite sequencing (RRBS) and RNA-seq, we concluded that CRISPR-Cas SunTag-directed DNMT3A methylated regions of interest without affecting global DNA methylome and transcriptome. This effective and precise tool enables site-specific manipulation of DNA methylation and may be used to address the relationship beteween DNA methylation and gene expression. Disclosures No relevant conflicts of interest to declare.

Epigenetic Modification Can Regulate the Stem Cell State of Hematopoietic Cells.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1356-1356
Author(s):  
Il-Hoan Oh ◽  
Hye-Jung Kim ◽  
Yun Shin Chung
Keyword(s):  
Dna Methylation ◽  
Stem Cell ◽  
De Novo ◽  
Epigenetic Modification ◽  
Hematopoietic Cells ◽  
Self Renewal ◽  
Hematopoietic Stem ◽  
Cd34 Cells ◽  
Marrow Cells

Abstract The maintenance of undifferentiated state and ability for self-renewal constitutes key properties of hematopoietic stem cell (HSC). To explore the possibility that epigenetic modification contributes to regulation of HSC functions, we have studied whether distinctive epigenetic modification can be correlated to different functions of hematopoietic cells. As a first approach, the global DNA methylations in non-coding repetitive elements were examined using mIAP, mEtn, and mc.satellite regions as marker loci. Sequencing of sodium bisulfite-modified CpG islands in these loci showed that most primitive Lin-c-kit+CD34− cells displayed highest level of DNA methylation as compared to the progenitor-enriched Lin-c-kit+CD34+ cells or differentiated counterpart (Lin+ cells) in mc satellite regions (85.7%, 60 %, 65%, respectively) and mEtn regions (73%, 58%, 74%, respectively), but not in mIAP region. Interestingly, whereas most primitive Lin-c-kit+CD34− cells expressed highest level of methyl cytosine binding protein (MeCp2) or DNA methyl transferase 3 (DNMT3a, 3b), the Lin+ cells expressed bare to minimal level of these gene products despite their high maintenance of DNA methylation, suggesting a differential de-novo methylations between these cells. Similarly, the most primitive Lin-c-kit+CD34− cells exhibited highest level of total acetylated histone (Ac-H4) but these cells expressed also high levels of histone deacetylase (HDAC) as well as histone acetyl transferase (HAT). Subsequent pulse-labeling with C14-acetate demonstrated that immature bone marrow cells (lin-), but not mature Lin+ cells, exhibited active acetylation of H4 with higher turn-overs, thus showing active remodeling of chromatin structures in immature hematopoietic cells. Next, to explore whether alterations in epigenetic modification could influence HSC function, the effect of epigenetic blockers (5-Azacytidine or TSA) were examined for their influence on in-vivo self-renewing activity of transplanted HSCs. Thus, recipients that had been lethally irradiated and transplanted with congeneic HSCs were treated with blockers during first two weeks of recovery, and transplanted into secondary recipients 18 weeks later to determine CRU numbers regenerated. The result of this CRU assay revealed that HSCs had underwent 32-folds higher self-renewal with inhibition of HDAC (22 vs. 738 CRUs), and 11-folds higher self-renewal with inhibition of DNA methylation (22 vs. 248 CRUs) showing that self-renewing potential of “stimulated” HSC is regulated by epigenetic modification. Next, to see if stem cell fate can be also influenced by epigenetic reprogramming, the effects of epigenetic blockers during “stationary” phase of hematopoiesis were examined by treating donor mice with epigenetic blockers for 3 weeks before sacrifice. Limiting dilution transplantation of these marrows revealed that the CRU frequencies in the treated (5-Azacytidine + TSA) donor marrows were 7-folds higher compared to the un-treated donor marrow cells (1/22,9000 vs. 1/3000) in the absence of increase in total marrow cell numbers, suggesting de-novo generation of CRUs with epigenetic manipulations. Taken together, these results show that the epigenetic modification should be an important regulatory mechanism for self-renewal and fate decisions for normal HSCs in-vivo.

scholarly journals DNA Methylation Diversification at the Integrated Organellar DNA-Like Sequence

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 602 ◽  
Author(s):  
Takanori Yoshida ◽  
Yoshiaki Tarutani ◽  
Tetsuji Kakutani ◽  
Akira Kawabe
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Epigenetic Modification ◽  
Natural Populations ◽  
Nuclear Genome ◽  
Amplicon Sequencing ◽  
Epigenetic Modifications ◽  
Plant Genome ◽  
Organellar Dna ◽  
Epigenetic Diversity

Plants have a lot of diversity in epigenetic modifications such as DNA methylation in their natural populations or cultivars. Although many studies observing the epigenetic diversity within and among species have been reported, the mechanisms how these variations are generated are still not clear. In addition to the de novo spontaneous epi-mutation, the intra- and inter-specific crossing can also cause a change of epigenetic modifications in their progenies. Here we report an example of diversification of DNA methylation by crossing and succeeding selfing. We traced the inheritance pattern of epigenetic modification during the crossing experiment between two natural strains Columbia (Col), and Landsberg electa (Ler) in model plant Arabidopsis thaliana to observe the inheritance of DNA methylation in two organellar DNA-like sequence regions in the nuclear genome. Because organellar DNA integration to the nuclear genome is common in flowering plants and these sequences are occasionally methylated, such DNA could be the novel source of plant genome evolution. The amplicon sequencing, using bisulfite-converted DNA and a next-generation auto-sequencer, was able to efficiently track the heredity of DNA methylation in F1 and F2 populations. One region showed hypomethylation in the F1 population and succeeding elevation of DNA methylation with large variance in the F2 population. The methylation level of Col and Ler alleles in F2 heterozygotes showed a significant positive correlation, implying the trans-chromosomal effect on DNA methylation. The results may suggest the possible mechanism causing the natural epigenetic diversity within plant populations.

scholarly journals Differential Recruitment of Methylated CpG Binding Domains by the Orphan Receptor GCNF Initiates the Repression and Silencing of Oct4 Expression

2006 ◽  
Vol 26 (24) ◽  
pp. 9471-9483 ◽  
Author(s):  
Peili Gu ◽  
Damien Le Menuet ◽  
Arthur C.-K. Chung ◽  
Austin J. Cooney
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Epigenetic Modification ◽  
Es Cells ◽  
Somatic Cells ◽  
Embryonic Stem ◽  
Orphan Receptor ◽  
Proximal Promoter ◽  
Es Cell ◽  
Oct4 Expression

ABSTRACT The pluripotent factor Oct4 is a key transcription factor that maintains embryonic stem (ES) cell self-renewal and is down-regulated upon the differentiation of ES cells and silenced in somatic cells. A combination of cis elements, transcription factors, and epigenetic modifications, such as DNA methylation, are involved in the regulation of Oct4 gene expression. Here we show that the orphan nuclear receptor GCNF initiates Oct4 repression and DNA methylation by the differential recruitment of MBD (methylated CpG binding domain) factors to the promoter. Compared with wild-type ES cells and gastrulating embryos, Oct4 repression is lost and its proximal promoter is significantly hypomethylated in RA-differentiated GCNF−/− ES cells. The Oct4 gene is reexpressed in some somatic cells of GCNF−/− embryos, showing that it has not been properly silenced coincident with reduced DNA methylation of its promoter. Efforts to characterize mediators of GCNF's repressive function and DNA methylation of the Oct4 promoter identified methyl-DNA binding proteins, MBD3 and MBD2, as GCNF-interacting factors. In P19 and ES cells, upon differentiation, endogenous GCNF binds to the Oct4 proximal promoter and differentially recruits MBD3 and MBD2. In differentiated GCNF−/− ES cells, recruitment of MBD3 and MBD2 to the Oct4 promoter is lost, and repression of Oct4 expression and DNA methylation fails to occur. RNA interference-mediated knockdown of MBD3 and/or MBD2 expression results in reduced Oct4 repression in differentiated P19 and ES cells. Repression of Oct4 expression and recruitment of MBD3 are maintained in de novo DNA methylation-deficient ES cells (Dnmt3A/3B-null cells), while MBD2 recruitment is lost. Thus, recruitment of MBD3 and MBD2 by GCNF links two events, gene-specific repression and DNA methylation, which occur differentially at the Oct4 promoter. GCNF initiates the repression and epigenetic modification of Oct4 gene during ES cell differentiation.

scholarly journals DNA methylation in the pathogenesis of polycystic ovary syndrome

Reproduction ◽  
2019 ◽  
Vol 158 (1) ◽  
pp. R27-R40 ◽  
Author(s):  
Edgar Ricardo Vázquez-Martínez ◽  
Yadira Inés Gómez-Viais ◽  
Elizabeth García-Gómez ◽  
Christian Reyes-Mayoral ◽  
Enrique Reyes-Muñoz ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Polycystic Ovary Syndrome ◽  
Polycystic Ovary ◽  
Epigenetic Modification ◽  
Premenopausal Women ◽  
Abnormal Development ◽  
Ovary Syndrome ◽  
Hormone Synthesis ◽  
Glucose And Lipid Metabolism ◽  
The Impact

Polycystic ovary syndrome (PCOS) is the leading endocrine and metabolic disorder in premenopausal women characterized by hyperandrogenism and abnormal development of ovarian follicles. To date, the PCOS etiology remains unclear and has been related to insulin resistance, obesity, type 2 diabetes mellitus, cardiovascular disease and infertility, among other morbidities. Substantial evidence illustrates the impact of genetic, intrauterine and environmental factors on the PCOS etiology. Lately, epigenetic factors have garnered considerable attention in the pathogenesis of PCOS considering that changes in the content of DNA methylation, histone acetylation and noncoding RNAs have been reported in various tissues of women with this disease. DNA methylation is changed in the peripheral and umbilical cord blood, as well as in ovarian and adipose tissue of women with PCOS, suggesting the involvement of this epigenetic modification in the pathogenesis of the disease. Perhaps, these defects in DNA methylation promote the deregulation of genes involved in inflammation, hormone synthesis and signaling and glucose and lipid metabolism. Research on the role of DNA methylation in the pathogenesis of PCOS is just beginning, and several issues await investigation. This review aims to provide an overview of current research focused on DNA methylation and PCOS, as well as discuss the perspectives regarding this topic.

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