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

By D. Globisch, M. Münzel, Markus Müller, S. Michalakis, Mirko Wagner, Susanne F. Koch, Tobias Brückl, M. Biel, T. Carell. PLoS ONE, 2010

860 citations recorded by the source corpus.

5–Hydroxymethylcytosine (hmC) was recently detected as the sixth base in mammalian tissue at so far controversial levels. The function of the modified base is currently unknown, but it is certain that the base is generated from 5-methylcytosine (mC). This fuels the hypothesis that it represents an intermediate of an active demethylation process, which could involve further oxidation of the hydroxymethyl group to a formyl or carboxyl group followed by either deformylation or decarboxylation. Here, we use an ultra-sensitive and accurate isotope based LC-MS method to precisely determine the levels of hmC in various mouse tissues and we searched for 5–formylcytosine (fC), 5-carboxylcytosine (caC), and 5–hydroxymethyluracil (hmU) as putative active demethylation intermediates. Our data suggest that an active oxidative mC demethylation pathway is unlikely to occur. Additionally, we show using HPLC-MS analysis and immunohistochemistry that hmC is present in all tissues and cell types with highest concentrations in neuronal cells of the CNS.

Subfields: Biochemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0aa140be1f222599e506e963ac86afb0c1cb49f9

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In Molecular Biology

1. Hao Wu
2. Yi Zhang
3. Chuan He
4. Wolf Reik
5. Qing Dai
6. Peng Jin
7. Chun-Xiao Song
8. G. Fan

Citations in the corpus

• Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair (2011, neutral): “, 2009), has been proposed as a demethylation intermediate (Globisch et al., 2010; Wu and Zhang, 2010).”
• Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. (2011, background): “…C); medium levels in kidney, nasal epithelia, bladder, heart, muscle, and lung (1.5 3 103 to 1.7 3 103 5hmC in every 106 C); and low levels in pituitary gland, liver, spleen, and testes (0.3 3 103 to 0.6 3 103 5hmC in 2438 GENES & DEVELOPMENT every 106 C) (Munzel et al. 2010; Globisch et al. 2011).”
• Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions (2014, positive): “Supporting the physiological relevance of TET-mediated 5mC oxidation, 5hmC can be readily detected in most cell-types (1%–5% of 5mC) and is particularly enriched in the genome of adult neurons (15%–40% of 5mC) (Globisch et al., 2010; Kriaucionis and Heintz, 2009).”
• 5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging (2011, background): “In the CNS, 5-hmC is substantially enriched relative to many other tissues and cell types; for instance, 5-hmC levels in the brain are approximately tenfold greater than those seen in ES cell”
• Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome (2012, neutral): “5hmC was found to be widespread in many tissues and cell types, although with diverse levels of abundance (Globisch et al., 2010; Munzel et al., 2010; Song et al., 2011; Szwagierczak et al., 2010).”
• DNA Demethylation Dynamics (2011, background): “5hmC is especially abundant in tissues such as brain and in pluripotent embryonic stem cells (ESCs), but it is also present at lower levels in blood, lung, kidney, and muscle (Globisch et al., 2010; Kriaucionis and Heintz, 2009; Ruzov et al., 2011; Song et al., 2011; Tahiliani et al., 2009).”
• Uncovering the role of 5-hydroxymethylcytosine in the epigenome (2011, background): “7% and are highest in tissues from the central nervous syste”
• Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. (2013, neutral): “This modification is particularly abundant in the brain and in embryonic stem cells but is detectable in all tissues tested (Globisch et al., 2010; Szwagierczak et al., 2010).”
• DNA Methylation and Its Basic Function (2013, methodology): “…of distinguishing 5hmC from 5mC in the genome: CpG endlabeling followed by thin-layer chromatography (Tahiliani et al, 2009) and high-performance liquid chromatography (HPLC) with either UV detection (Liutkeviciute et al, 2009) or tandem mass spectrometry (Globisch et al, 2010; Le et al, 2011).”