Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA

Szwagierczak, Aleksandra; Bultmann, Sebastian; Schmidt, Christine S.; Spada, Fabio; Leonhardt, Heinrich

doi:10.1093/nar/gkq684

Cited by 397 publications

(394 citation statements)

References 15 publications

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“…Tet1-mediated accumulation of 5-hmC is critically involved in neuronal differentiation and in the reprogramming of pluripotent stem cells (33), thus suggesting a distinct role for Tet1 during early brain development. Tet3, in contrast, is the most highly expressed isoform in the adult cortex (30), and the highest level of 5-hmC in the adult brain is found in cortical neurons (7), where it continues to accumulate across the lifespan (9). Together, these data suggest a potential developmental stage-and/or region-specific function for each Tet isoform and its influence on the regulation of 5-hmC, which would be difficult to disentangle from the use of mice that have had Tet1 knockout throughout early development.…”

Section: Discussionmentioning

confidence: 94%

“…Recent evidence indicates that Tet1 promotes active DNA demethylation in the adult hippocampus (8) and that the accumulation of 5-hmC and associated effects on gene expression are involved in adult neurogenesis, spatial learning, and the extinction of contextual fear (27)(28)(29). In contrast, Tet3 is highly expressed in the adult cortex (30), although its function with respect to fear extinction memory has yet to be determined. We therefore set out to explore the role of Tet3-mediated hydroxylation within the ILPFC and to elucidate whether it is involved in the rapid behavioral adaptation supporting the extinction of conditioned fear.…”

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confidence: 99%

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Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation

Wei

Zhao

et al. 2014

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

167

166

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5-hydroxymethylcytosine (5-hmC) is a novel DNA modification that is highly enriched in the adult brain and dynamically regulated by neural activity. 5-hmC accumulates across the lifespan; however, the functional relevance of this change in 5-hmC and whether it is necessary for behavioral adaptation have not been fully elucidated. Moreover, although the ten-eleven translocation (Tet) family of enzymes is known to be essential for converting methylated DNA to 5-hmC, the role of individual Tet proteins in the adult cortex remains unclear. Using 5-hmC capture together with high-throughput DNA sequencing on individual mice, we show that fear extinction, an important form of reversal learning, leads to a dramatic genome-wide redistribution of 5-hmC within the infralimbic prefrontal cortex. Moreover, extinction learning-induced Tet3-mediated accumulation of 5-hmC is associated with the establishment of epigenetic states that promote gene expression and rapid behavioral adaptation.E pigenetic mechanisms are critically involved in the regulation of gene expression underlying learning and memory (1). Dynamic variation in the accumulation of a particular epigenetic mark, 5-methycytosine (5-mC), has emerged as a key factor in experience-dependent plasticity and the formation of fearrelated memory (2). However, 5-mC is not the only covalent modification of DNA in eukaryotes, as methylated cytosine guanine (CpG) dinucleotides can be successively oxidized and converted to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), and 5-carboxylcytosine by the Tet family of DNA dioxygenases (3, 4). Although little is known about the functional relevance of 5-fC and 5-carboxylcytosine (5, 6), an understanding of 5-hmC is starting to emerge. 5-hmC is highly enriched in the adult brain (7), dynamically regulated by neural activity (8), and accumulates across the lifespan (9). This epigenetic mark is critically involved in neuronal differentiation and in the reprogramming of pluripotent stem cells (10), and rather than being an intermediate state of active DNA demethylation, 5-hmC can be either dynamic or stable (8, 10). Unlike its repressive cousin, 5-mC, which is primarily found along CpG-rich gene promoters, 5-hmC is enriched within gene bodies and at intronexon boundaries of synaptic plasticity-related genes, as well as within distal cis-regulatory elements, which together point to an important role for 5-hmC in coordinating transcriptional activity (11-13). Thus, it is evident that the relationship between this particular covalent modification of DNA and gene expression is far more complex than currently realized.The inhibition of learned fear is an evolutionarily conserved behavioral adaptation that is essential for survival. This learning process, known as extinction, involves rapid reversal of previously learned contingencies, which depend on gene expression and protein synthesis. Impairments in the neural mechanisms that promote this beneficial response to threat can lead to the development of posttraumatic stress disorder ...

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Section: Discussionmentioning

confidence: 94%

mentioning

confidence: 99%

Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation

Wei

Zhao

et al. 2014

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

167

166

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“…4,6,7 Tet1 and Tet2 are highly expressed in mouse ES cells and are rapidly downregulated upon differentiation, 3,4,8 whereas Tet3 is expressed at very low levels in ES cells and upregulated during ES cell differentiation. Further analysis reveals that both Tet1 and Tet2 are downstream targets of key pluripotency factors.…”

Section: Genome-wide Occupancy Of Tet1 In Mouse Embryonic Stem Cellsmentioning

confidence: 99%

Tet1 and 5-hydroxymethylation

Zhang

2011

Cell Cycle

116

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“…7 To explore the relationship among TET2 mutations, global gene expression profiles (GEPs) and 5hmC levels, we measured 5hmC levels in the genomic DNA in a series of 30 sAML patients using a novel assay method employing b-glucosyltransferase from bacteriophage T4. 8 In addition to the TET2 mutational status, we screened for IDH1/2 mutations (see Supplementary Material).…”

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confidence: 99%