Stage-specific regulation of DNA methylation by TET enzymes during human cardiac differentiation

DNA methylation at enhancers and CpG islands usually leads to gene repression, which is counteracted by DNA demethylation through the TET protein family. However, how TET enzymes are recruited and regulated at these genomic loci is not fully understood. Here, we identify TET2, the glycosyltransferase OGT and a previously undescribed proline and serine rich protein, PROSER1 as interactors of UTX, a component of the enhancer-associated MLL3/4 complexes. We find that PROSER1 mediates the interaction between OGT and TET2, thus promoting TET2 O-GlcNAcylation and protein stability. In addition, PROSER1, UTX, TET1/2, and OGT colocalize on many genomic elements genome-wide. Loss of PROSER1 results in lower enrichment of UTX, TET1/2, and OGT at enhancers and CpG islands, with a concomitant increase in DNA methylation and transcriptional down-regulation of associated target genes and increased DNA hypermethylation encroachment at H3K4me1-predisposed CpG islands. Furthermore, we provide evidence that PROSER1 acts as a more general regulator of OGT activity by controlling O-GlcNAcylation of multiple other chromatin signaling pathways. Taken together, this study describes for the first time a regulator of TET2 O-GlcNAcylation and its implications in mediating DNA demethylation at UTX-dependent enhancers and CpG islands and supports an important role for PROSER1 in regulating the function of various chromatin-associated proteins via OGT-mediated O-GlcNAcylation.

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Tet2 negatively regulates memory fidelity

10.1101/843581 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kristine E. Zengeler ◽

Caroline P. Gettens ◽

Hannah C. Smith ◽

Mallory M. Caron ◽

Xinyuan Zhang ◽

...

Keyword(s):

Dna Methylation ◽

Bisulfite Sequencing ◽

Memory Formation ◽

Negative Regulator ◽

Long Term Memory ◽

Term Memory ◽

Glutamatergic Neurons ◽

Genome Bisulfite Sequencing ◽

Tet Enzymes

SummaryDespite being fully differentiated, DNA methylation is dynamically regulated in post-mitotic glutamatergic neurons in the CA1 of the hippocampus through competing active DNA methylation and de-methylation, a process that regulates neuronal plasticity. Active DNA methylation after learning is necessary for long-term memory formation, and active DNA de-methylation by the TET enzymes has been implicated as a counter-regulator of that biochemical process. We demonstrate that Tet2 functions in the CA1 as a negative regulator of long-term memory, whereby its knockdown across the CA1 or haploinsufficiency in glutamatergic neurons enhances the fidelity of hippocampal-dependent spatial and associative memory. Loci of altered DNA methylation were then determined using whole genome bisulfite sequencing from glutamatergic Tet2 haploinsufficient CA1 tissue, which revealed hypermethylation in the promoters of genes known to be transcriptionally regulated after experiential learning. This study demonstrates a link between Tet2 activity at genes important for memory formation in CA1 glutamatergic neurons and memory fidelity.

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S137 DNA METHYLATION DYNAMICS IDENTIFY LINEAGE-SPECIFIC REGULATION PATTERNS OF HEMATOPOIETIC DIFFERENTIATION

HemaSphere ◽

10.1097/01.hs9.0000558768.40633.0a ◽

2019 ◽

Vol 3 (S1) ◽

pp. 20

Author(s):

S. Stäble ◽

S. Krämer ◽

J. Langstein ◽

R. Bogeska ◽

M. Hartmann ◽

...

Keyword(s):

Dna Methylation ◽

Hematopoietic Differentiation ◽

Specific Regulation

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Role of the DNA repair genes H2AX and HMGB1 in human fat distribution and lipid profiles

BMJ Open Diabetes Research & Care ◽

10.1136/bmjdrc-2019-000831 ◽

2020 ◽

Vol 8 (1) ◽

pp. e000831

Author(s):

Kerstin Rohde ◽

Torunn Rønningen ◽

Lars la Cour Poulsen ◽

Maria Keller ◽

Matthias Blüher ◽

...

Keyword(s):

Dna Methylation ◽

Dna Repair ◽

Density Lipoprotein ◽

Fat Distribution ◽

Lipoprotein Cholesterol ◽

Mrna Levels ◽

Dna Repair Genes ◽

Specific Regulation ◽

Repair Genes

IntroductionRegional fat distribution strongly relates to metabolic comorbidities. We identified the DNA repair genes H2AX and HMGB1 to be differentially expressed between human subcutaneous (SAT) and omental visceral adipose tissue (OVAT) depots. As increased DNA damage is linked to metabolic disease, we here sought to analyze whether depot-specific H2AX and HMGB1 expression is related to anthropometric and metabolic profiles of obesity. We further tested for different H2AX mRNA regulatory mechanisms by analyzing promoter DNA methylation and genotyped rs7350 in the H2AX locus.Research design and methodsGene expression (OVAT n=48; SAT n=55) and DNA promoter methylation data (OVAT and SAT n=77) were extracted from an existing dataset as described elsewhere. Genotype data for the 3’untranslated region (3’UTR) H2AX variant rs7350 were generated by using the TaqMan genotyping system in 243 subjects of the same cohort. Statistical analyses were done using SPSS statistics software 24 and GraphPad Prism 6.ResultsWe identified H2AX being higher (p=0.002) and HMGB1 being less expressed (p=0.0001) in OVAT compared with SAT. Further, we observed positive interdepot correlations of OVAT and SAT for both HMGB1 (p=1×10–6) and H2AX mRNA levels (p=0.024). Depot-specific associations were observed for both genes’ methylation levels with either high density lipoprotein cholesterol, low density lipoprotein cholesterol, triglycerides and/or with OVAT/SAT-ratio (all p<0.05). A significantly lower level of total cholesterol in minor A-Allele carriers of rs7350 compared with AG and GG carriers (p=0.001) was observed. Additionally, subjects carrying the A-allele showed lower SAT HMGB1 expression level (p=0.030).ConclusionOur results suggest a fat depot-specific regulation of H2AX and HMGB1 potentially mediated by both DNA methylation and genetic variation. Rs7350, DNA methylation and/or mRNA levels of H2AX and HMGB1 are related to lipid parameters. Further studies are warranted to evaluate the functional role of the DNA repair genes H2AX and HMGB1 in obesity and fat distribution.

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The Competition between DNA Methylation and Demethylation is Associated with Transcription Regulation and Tumorigenesis

10.21203/rs.3.rs-123209/v1 ◽

2021 ◽

Author(s):

Wei Li ◽

Jiejun Shi ◽

Jianfeng Xu ◽

Yiling Chen ◽

Jingyi Jessica Li ◽

...

Keyword(s):

Dna Methylation ◽

Transcription Regulation ◽

Tumor Suppressor Genes ◽

Strong Association ◽

Promoter Hypermethylation ◽

Dna Methyltransferases ◽

Chromatin Accessibility ◽

Strongly Correlated ◽

Average Methylation ◽

Tet Enzymes

Abstract The mammalian DNA methylome is formed by two antagonizing processes, methylation by DNA methyltransferases (DNMT) and demethylation by ten-eleven translocation (TET) dioxygenases. Although the dynamics of either methylation or demethylation have been intensively studied in the past decade, their competition effect remains elusive. Here, we quantify the competition between DNA methylation and demethylation by the percentage of unmethylated CpGs within a partially methylated read from bisulfite sequencing. After verifying methylation competition by its strong association with the co-localization of DNMT and TET enzymes, we observe that methylation competition is strongly correlated with gene expression. In particular, during tumorigenesis, the elevation of methylation competition is associated with the repression of 40 ~ 60% of tumor suppressor genes, which cannot be explained by promoter hypermethylation alone. Furthermore, methylation competition can be used to stratify large undermethylated regions with negligible differences in average methylation into two subgroups with distinct chromatin accessibility and gene regulation patterns. Together, methylation competition represents a novel methylation metric important for transcription regulation and tumorigenesis and is largely distinct from conventional metrics, such as average methylation and methylation variation.

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Oxidative DNA demethylation mediated by Tet enzymes

National Science Review ◽

10.1093/nsr/nwv029 ◽

2015 ◽

Vol 2 (3) ◽

pp. 318-328 ◽

Cited By ~ 19

Author(s):

Guo-Liang Xu ◽

Jiemin Wong

Keyword(s):

Dna Methylation ◽

Developmental Regulation ◽

Cell Lineage ◽

Dna Demethylation ◽

Dna Modification ◽

Mammalian Development ◽

Research Focus ◽

Dynamic Changes ◽

Tet Enzymes ◽

Intense Research

Abstract DNA modification, methylation of cytosine (5mC), and oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) can have profound effects on genome function in animals. These modifications are intricately involved in DNA methylation reprograming dynamics during mammalian development. Together, they contribute to cell lineage restriction and maintenance, while also undergoing dynamic changes during cellular transitions and induced reprograming. The last five years have seen an intense research focus on enzymatic DNA demethylation, triggered by the discovery of 5hmC and Tet dioxygenases. In this review, we evaluate recent findings that have provided new insights into the mechanisms underlying DNA demethylation and its effect on developmental regulation.

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Abstract 15945: Temporal Analyses of Chromatin Accessibility, Dna Methylation and Epigenomic Structure Identify Mechanisms of Locus-specific Regulation in the Heart

Circulation ◽

10.1161/circ.142.suppl_3.15945 ◽

2020 ◽

Vol 142 (Suppl_3) ◽

Author(s):

Manuel Rosa-garrido ◽

Douglas J Chapski ◽

Maximilian Cabaj ◽

Marco Morselli ◽

Shuxun Ren ◽

...

Keyword(s):

Gene Expression ◽

Heart Failure ◽

Dna Methylation ◽

Transcription Factors ◽

Pressure Overload ◽

Structural Data ◽

Chromatin Accessibility ◽

Noncoding Regions ◽

Specific Regulation ◽

Time Point

Heart failure can be induced or ameliorated in animal models by regulation of chromatin modifying enzymes, yet the chromatin level actions of these enzymes during pathogenesis is unknown. Because many histone modifiers and transcription factors regulate gene expression, we sought to directly measure chromatin accessibility through an unbiased method (ATAC-seq) that reports the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, primarily in noncoding regions. The majority of changes that persisted to the decompensated phase (3weeks) were already established at the earlier time point, revealing a temporal nature of epigenomic compensation to pathologic stimuli. A cardiac-specific CTCF depletion model was used to examine basal cardiac chromatin function and revealed that disruption of this structure by loss of CTCF causes widespread changes in accessibility and methylation distinct from those in pressure overload. Less than half of the gene expression changes occurring at either time point after pressure overload were explained by DNA methylation alone and accessibility was likewise an imperfect predictor of transcription. Distal enhancers were paired with genes based on chromatin structural data and the regulatory actions of these elements examined in the context of DNA methylation and accessibility: enhancer actions require specific combinations of transcription factors and histone modifications at different stages of disease and to execute aspecific transcriptional event (methylation or accessibility alone was insufficient to predict the behavior). For example, the subset of differentially accessible enhancers in both 3 weeks TACand CTCF depletion significantly overlaps with cardiac transcription factors Gata4 (p=4.13x10 -6 ),Nkx2-5 (p=2.49x10 -5 ) and P300 (p=8.38x10 -7 ). In summary, these studies characterize the logic employed at coding, regulatory, and noncoding regions to regulate chromatin accessibility and transcription, providing a resource of epigenomic data at distinct temporal stages of heart failure.

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Neuroprotective Effect of Piracetam against Cocaine-Induced Neuro Epigenetic Modification of DNA Methylation in Astrocytes

Brain Sciences ◽

10.3390/brainsci10090611 ◽

2020 ◽

Vol 10 (9) ◽

pp. 611

Author(s):

Kalaiselvi Sivalingam ◽

Thangavel Samikkannu

Keyword(s):

Dna Methylation ◽

Nuclear Dna ◽

Epigenetic Modification ◽

Neuroprotective Effect ◽

Dna Methyltransferases ◽

Epigenetic Changes ◽

Nootropic Drug ◽

The Central Nervous System ◽

Tet Enzymes ◽

The Impact

Cocaine abuse is known to alter mitochondrial biogenesis and induce epigenetic modification linked with neuronal dysfunction. Cocaine-induced epigenetic modification of DNA methylation and the mitochondrial genome may affect mitochondrial DNA (mtDNA) and nuclear DNA (nDNA), as epigenetic DNA methylation is key to maintaining genomic integrity in the central nervous system (CNS). However, the impact of cocaine-mediated epigenetic changes in astrocytes has not yet been elucidated. In this study, we explored the neuroprotective effect of piracetam against cocaine-induced epigenetic changes in DNA methylation in astrocytes. To study our hypothesis, we exposed human astrocytes to cocaine alone or in combination with the nootropic drug piracetam. We examined the expression of the DNA methyltransferases (DNMTs) DNMT-1, DNMT-3A, and DNMT-3B; global DNA methylation levels of 5-methycytosine (5-mC); and induction of ten–eleven translocation (TET) enzymes in astrocytes. In addition, we analyzed mtDNA methylation by targeted next-generation bisulfite sequencing. Our data provide evidence that cocaine impairs DNMT activity and thereby has impacts on mtDNA, which might contribute to the neurodegeneration observed in cocaine users. These effects might be at least partially prevented by piracetam, allowing neuronal function to be maintained.

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Effect of diabetes status and hyperglycemia on global DNA methylation and hydroxymethylation

Endocrine Connections ◽

10.1530/ec-17-0199 ◽

2017 ◽

Vol 6 (8) ◽

pp. 708-725 ◽

Cited By ~ 17

Author(s):

Jairo Arturo Pinzón-Cortés ◽

Angelina Perna-Chaux ◽

Nicolás Steven Rojas-Villamizar ◽

Angélica Díaz-Basabe ◽

Diana Carolina Polanía-Villanueva ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Peripheral Blood ◽

Target Organ Damage ◽

Organ Damage ◽

Dna Demethylation ◽

Global Dna Methylation ◽

Dna Hydroxymethylation ◽

Diabetes Status ◽

Tet Enzymes

Type 2 diabetes mellitus (T2DM) is characterized by oxidative stress that could lead to chronic micro- and macrovascular complications. We hypothesized that some of the target organ damage is mediated by oxidative alterations in epigenetic mechanisms involving DNA methylation (5mC) and DNA hydroxymethylation (5hmC). We analyzed global DNA methylation and hydroxymethylation in peripheral blood cells in well-controlled and poorly controlled patients with T2DM and compared them with healthy controls. We also analyzed microarrays of DNA methylation and gene expression of other important tissues in the context of diabetes from the GEO database repository and then compared these results with our experimental gene expression data. DNA methylation and, more importantly, DNA hydroxymethylation levels were increased in poorly controlled patients compared to well-controlled and healthy individuals. Both 5mC and 5hmC measurements were correlated with the percentage of glycated hemoglobin, indicating a direct impact of hyperglycemia on changes over the epigenome. The analysis of methylation microarrays was concordant, and 5mC levels were increased in the peripheral blood of T2DM patients. However, the DNA methylation levels were the opposite of those in other tissues, such as the pancreas, adipose tissue and skeletal muscle. We hypothesize that a process of DNA oxidation associated with hyperglycemia may explain the DNA demethylation in which the activity of ten-eleven translocation (TET) proteins is not sufficient to complete the process. High levels of glucose lead to cellular oxidation, which triggers the process of DNA demethylation aided by TET enzymes, resulting in epigenetic dysregulation of the damaged tissues.

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Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1608679113 ◽

2016 ◽

Vol 113 (43) ◽

pp. 12202-12207 ◽

Cited By ~ 82

Author(s):

Timothy Alexander Hore ◽

Ferdinand von Meyenn ◽

Mirunalini Ravichandran ◽

Martin Bachman ◽

Gabriella Ficz ◽

...

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Retinoic Acid ◽

Induced Pluripotent Stem Cells ◽

Pluripotent Stem Cells ◽

Embryonic Stem ◽

Epigenetic Memory ◽

Mechanistic Insight ◽

Induced Pluripotent ◽

Tet Enzymes

Epigenetic memory, in particular DNA methylation, is established during development in differentiating cells and must be erased to create naïve (induced) pluripotent stem cells. The ten-eleven translocation (TET) enzymes can catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives, thereby actively removing this memory. Nevertheless, the mechanism by which the TET enzymes are regulated, and the extent to which they can be manipulated, are poorly understood. Here we report that retinoic acid (RA) or retinol (vitamin A) and ascorbate (vitamin C) act as modulators of TET levels and activity. RA or retinol enhances 5hmC production in naïve embryonic stem cells by activation of TET2 and TET3 transcription, whereas ascorbate potentiates TET activity and 5hmC production through enhanced Fe2+ recycling, and not as a cofactor as reported previously. We find that both ascorbate and RA or retinol promote the derivation of induced pluripotent stem cells synergistically and enhance the erasure of epigenetic memory. This mechanistic insight has significance for the development of cell treatments for regenenerative medicine, and enhances our understanding of how intrinsic and extrinsic signals shape the epigenome.

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