Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

Globisch, Daniel; Münzel, Martin; Müller, Markus; Michalakis, Stylianos; Wagner, Mirko; Koch, Susanne; Brückl, Tobias; Biel, Martin; Carell, Thomas

doi:10.1371/journal.pone.0015367

Cited by 753 publications

(762 citation statements)

References 34 publications

(54 reference statements)

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“…Using a LC-MS/MS method in the present study, we find that 5hmC contents varies among spermatogenic cells with the lowest in pacSC, rST and eST (0.03B0.04%) and the highest in SG-A and SG-B (0.08-0.10%). That the ratio of 5hmC/C in whole testes by Globisch et al 41 match well with our values in pacSC and rST reflects the fact that the adult testis is dominated by meiotic and post-meiotic cells. It is noteworthy that mESCs have similar levels to most germ cells except for rST and eST.…”

Section: Article Nature Communications | Doi: 101038/ncomms2995supporting

confidence: 92%

“…Interestingly, 5mC levels are constant from priSG-A to SZ and are comparable to that in mESCs ( Supplementary Fig. S7), again, consistent with what Globisch et al 41 observed among different ARTICLE tissues including testes. Therefore, 5hmC, which is approximately o2.5% of 5mC in spermatogenic cells, represents a small but dynamic portion of 5mC during spermatogenesis.…”

Section: Article Nature Communications | Doi: 101038/ncomms2995supporting

confidence: 89%

“…According to a previous study by Globisch et al 41 using HPLC-MS, the 5hmC contents in the spinal cord and testis were estimated to be 0.46 and 0.03% of C, respectively. Using a LC-MS/MS method in the present study, we find that 5hmC contents varies among spermatogenic cells with the lowest in pacSC, rST and eST (0.03B0.04%) and the highest in SG-A and SG-B (0.08-0.10%).…”

Section: Article Nature Communications | Doi: 101038/ncomms2995mentioning

confidence: 98%

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Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis

et al. 2013

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Little is known about how patterns of DNA methylation change during mammalian spermatogenesis. 5hmC has been recognized as a stable intermediate of DNA demethylation with potential regulatory functions in the mammalian genome. However, its global pattern in germ cells has yet to be addressed. Here, we first conducted absolute quantification of 5hmC in eight consecutive types of mouse spermatogenic cells using liquid chromatographytandem mass spectrometry, and then mapped its distributions in various genomic regions using our chemical labeling and enrichment method coupled with deep sequencing. We found that 5hmC mapped differentially to and changed dynamically in genomic regions related to expression regulation of protein-coding genes, piRNA precursor genes and repetitive elements. Moreover, 5hmC content correlated with the levels of various transcripts quantified by RNA-seq. These results suggest that the highly ordered alterations of 5hmC in the mouse genome are potentially crucial for the differentiation of spermatogenic cells.

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Section: Article Nature Communications | Doi: 101038/ncomms2995supporting

confidence: 92%

Section: Article Nature Communications | Doi: 101038/ncomms2995supporting

confidence: 89%

Section: Article Nature Communications | Doi: 101038/ncomms2995mentioning

confidence: 98%

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Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis

et al. 2013

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“…Current data indicate that hmC is substantially enriched in CNS neurons compared with other cell types, with hmC levels being ∼10-fold greater in the brain than in ES cells (31,32) and with CG hydroxymethylation (hmCG) accounting for 25% and 40% of all modified CG dinucleotides in the frontal cortex and cerebellum, respectively (8,29,33). Brain hmCG levels increase postnatally in parallel with mCH, with an approximately fourfold increase in abundance within the first 6 weeks after birth (8,34).…”

mentioning

confidence: 99%

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

Kinde

Gabel

Gilbert

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

209

198

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DNA methylation at CpG dinucleotides is an important epigenetic regulator common to virtually all mammalian cell types, but recent evidence indicates that during early postnatal development neuronal genomes also accumulate uniquely high levels of two alternative forms of methylation, non-CpG methylation and hydroxymethylation. Here we discuss the distinct landscape of DNA methylation in neurons, how it is established, and how it might affect the binding and function of protein readers of DNA methylation. We review studies of one critical reader of DNA methylation in the brain, the Rett syndrome protein methyl CpG-binding protein 2 (MeCP2), and discuss how differential binding affinity of MeCP2 for non-CpG and hydroxymethylation may affect the function of this methyl-binding protein in the nervous system.M ethylation of cytosines at the carbon 5 position (5-methylcytosine, mC) constitutes the most common covalent modification of vertebrate genomic DNA. Traditionally, cytosine methylation in vertebrate genomes has been viewed as largely restricted to CpG dinucleotide (CG) sequences, providing a stable epigenetic mark that mediates long-term transcriptional silencing. Indeed, 60-90% of all CGs are methylated in mammalian genomes, and CG methylation (mCG) has been shown to play critical roles in genomic imprinting, X-chromosome inactivation, cellular differentiation, and development (1). In addition, the disruption of cellular DNA methylation patterns has been linked to human disease, including multiple cancers (2, 3).Evidence that DNA methylation has a uniquely important role in the brain emerged almost two decades ago with the discovery of the prominent methyl-DNA-binding protein, methyl-CpG-binding protein 2 (MeCP2), and the later identification that mutations in MeCP2 give rise to the X-linked neurological disorder Rett syndrome (RTT) (4-6). Subsequent studies also have identified neurodevelopmental disorders associated with mutations in DNA methyltransferases (7), suggesting that both the enzymatic "writers" of DNA methylation patterns and the "readers" of these marks have important roles in the brain. In this context, new studies from several laboratories have uncovered extensive cytosine modification in the brain beyond mCG. Non-CG methylation (CH methylation or mCH, in which H = A, C, or T) is now appreciated to accumulate in the human and mouse brain postnatally, reaching levels similar to that of mCG in the neuronal genome (8, 9). Moreover, oxidation of mC by the ten-eleven translocation (Tet) family of dioxygenases leads to the selective accumulation of 5-hydroxymethylcytosine (hmC) in the adult brain, together with its more highly oxidized derivatives 5-formylcytosine and 5-carboxylcytosine (10, 11). This finding suggests that hmC may act as an intermediate in an active DNA demethylation pathway, though growing evidence also suggests that hmC may serve as a stable neuronal epigenetic mark in its own right (12).The discovery of these previously unidentified brain-enriched forms of DNA methylation provides...

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“…Scale bars: panorama 17 μm; inset 8 μm where it is thought to oppose the role of 5mC-mediated transcriptional repression by inhibiting the binding of methyl-CpG binding protein-2 and other DNA binding proteins; thus, 5hmC functions as a facilitator of geneexpression activity [44]. 5hmC might also be an intermediate of an active oxidative demethylation pathway [45], although metabolite evidence for this pathway is lacking [46]. Teneleven translocation methylcytosine dioxygenases (Teneleven translocation 1-3) are thought to be the oxidases that form 5hmC from 5mC [43].…”

Section: Dna Methylation As An Epigenetic Mechanismmentioning

confidence: 99%

Aberrant Regulation of DNA Methylation in Amyotrophic Lateral Sclerosis: A New Target of Disease Mechanisms

Martin

Wong

2013

Neurotherapeutics

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Amyotrophic lateral sclerosis (ALS) is the third most common adult-onset neurodegenerative disease. A diagnosis is fatal owing to degeneration of motor neurons in brain and spinal cord that control swallowing, breathing, and movement. ALS can be inherited, but most cases are not associated with a family history of the disease. The mechanisms causing motor neuron death in ALS are still unknown. Given the suspected complex interplay between multiple genes, the environment, metabolism, and lifestyle in the pathogenesis of ALS, we have hypothesized that the mechanisms of disease in ALS involve epigenetic contributions that can drive motor neuron degeneration. DNA methylation is an epigenetic mechanism for gene regulation engaged by DNA methyltransferase (Dnmt)-catalyzed methyl group transfer to carbon-5 in cytosine residues in gene regulatory promoter and nonpromoter regions. Recent genome-wide analyses have found differential gene methylation in human ALS. Neuropathologic assessments have revealed that motor neurons in human ALS show significant abnormalities in Dnmt1, Dnmt3a, and 5-methylcytosine. Similar changes are seen in mice with motor neuron degeneration, and Dnmt3a was found abundantly at synapses and in mitochondria. During apoptosis of cultured motor neuron-like cells, Dnmt1 and Dnmt3a protein levels increase, and 5-methylcytosine accumulates. Enforced expression of Dnmt3a, but not Dnmt1, induces degeneration of cultured neurons. Truncation mutation of the Dnmt3a catalytic domain and Dnmt3a RNAi blocks apoptosis of cultured neurons. Inhibition of Dnmt catalytic activity with small molecules RG108 and procainamide protects motor neurons from excessive DNA methylation and apoptosis in cell culture and in a mouse model of ALS. Thus, motor neurons can engage epigenetic mechanisms to cause their degeneration, involving Dnmts and increased DNA methylation. Aberrant DNA methylation in vulnerable cells is a new direction for discovering mechanisms of ALS pathogenesis that could be relevant to new disease target identification and therapies for ALS.

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Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

Cited by 753 publications

References 34 publications

Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis

Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

Aberrant Regulation of DNA Methylation in Amyotrophic Lateral Sclerosis: A New Target of Disease Mechanisms

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