Hydroxymethylation and its potential implication in DNA repair system: A review and future perspectives

Shukla, Ayush; Sehgal, Manika; Singh, Tiratha Raj

doi:10.1016/j.gene.2015.03.075

Cited by 44 publications

(36 citation statements)

References 91 publications

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“…Although proteins have been identified that specifically bind to 5hmC 25,26 , it is currently not known if these proteins can detect 5hmC sites strand-specifically. Thus, it is possible that 5hmC strand bias, and therefore strand age, may serve as a source of chromosome-wide epigenetic memory to determine downstream protein activity and instruct biological processes such as chromosome segregation 24 or DNA repair 27 . Thus, scAba-seq could be a complementary method to Strand-seq 28 for analyzing strand age and SCE events in cell types containing 5hmC.…”

Section: E T T E R Smentioning

confidence: 99%

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

et al. 2016

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The epigenetic DNA modification 5-hydroxymethylcytosine (5hmC) has crucial roles in development and gene regulation. Quantifying the abundance of this epigenetic mark at the single-cell level could enable us to understand its roles. We present a single-cell, genome-wide and strand-specific 5hmC sequencing technology, based on 5hmC glucosylation and glucosylation-dependent digestion of DNA, that reveals pronounced cell-to-cell variability in the abundance of 5hmC on the two DNA strands of a given chromosome. We develop a mathematical model that reproduces the strand bias and use this model to make two predictions. First, the variation in strand bias should decrease when 5hmC turnover increases. Second, the strand bias of two sister cells should be strongly anti-correlated. We validate these predictions experimentally, and use our model to reconstruct lineages of two- and four-cell mouse embryos, showing that single-cell 5hmC sequencing can be used as a lineage reconstruction tool.

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Section: E T T E R Smentioning

confidence: 99%

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

et al. 2016

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“…A question that must be elucidated is whether 5-hmC is just an intermediate product of the DNA demethylation process or if 5-hmC has a specific biological function. The association of 5-hmC with diseases, such as cancer (Orr et al 2012), neurological (Kato & Iwamoto 2014) and cardiovascular disorders (Barrick et al 2009), stem cell renewal (Shukla et al 2015), and gametogenesis and embryogenesis (Iqbal et al 2011) has been studied.…”

Section: Introductionmentioning

confidence: 99%

Distribution of 5-methylcytosine and 5-hydroxymethylcytosine in bovine fetal tissue of the placenta

et al. 2018

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5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) are modified cytosines found in mammals that are involved in the regulation of gene expression. The aim of this study was to characterize the global patterns of 5-mC and 5-hmC of the fetal placenta of Nellore cattle as well as blood and sperm as controls. 5-mC and 5-hmC levels were determined using MethylFlash Methylated/Hydroxymethylated DNA Quantification Kit, respectively. Placenta tissues showed lower levels of 5-mC and 5-hmC compared to sperm. The male cotyledon showed higher levels of 5-hmC than the female. For the first time, the levels of 5-mC and 5-hmC in Bos taurus indicus were characterized, which may contribute to our understanding of the mechanisms of epigenetic regulation in the placenta. The presence of 5-hmC in somatic tissues suggest that 5-hmC has its own biological function and it is not only a byproduct from the oxidation of 5-mC. These results may be of interest in ARTs, especially in cloning in the diagnosis/prognosis of aberrant placentation and the viability of pregnancies.

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“…C , cytosine; 5-mC , 5-methylcytosine; 5-hmC , 5-hydroxymethylcytosine; 5-fC , 5-formylcytosine; 5-caC , 5-carboxylcytosine; DNMT , DNA methyltransferase; Tet ; Ten-eleven translocation enzyme. (see also [53,54]).…”

Section: Figurementioning

confidence: 99%

The role of active DNA demethylation and Tet enzyme function in memory formation and cocaine action

Alaghband

Bredy

Wood

2016

Neuroscience Letters

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Active DNA modification is a major epigenetic mechanism that regulates gene expression in an experience-dependent manner, which is thought to establish stable changes in neuronal function and behavior. Recent discoveries regarding the Ten eleven translocation (Tet1-3) family of DNA hydroxylases have provided a new avenue for the study of active DNA demethylation, and may thus help to advance our understanding of how dynamic DNA modifications lead to long-lasting changes in brain regions underlying learning and memory, as well as drug-seeking and propensity for relapse following abstinence. Drug addiction is a complex, relapsing disorder in which compulsive drug-seeking behavior can persist despite aversive consequences. Therefore, understanding the molecular mechanisms that underlie the onset and persistence of drug addiction, as well as the pronounced propensity for relapse observed in addicts, is necessary for the development of selective treatments and therapies. In this mini-review, we provide an overview of the involvement of active DNA demethylation with an emphasis on the Tet family of enzymes and 5-hydroxymethylcytosine (5-hmC) in learning and memory, as well as in drug-seeking behavior. Memory and addiction share overlapping molecular, cellular, and circuit functions allowing research in one area to inform the other. Current discrepancies and directions for future studies focusing on the dynamic interplay between DNA methylation and demethylation, and how they orchestrate gene expression required for neuronal plasticity underlying memory formation, are discussed.

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Hydroxymethylation and its potential implication in DNA repair system: A review and future perspectives

Cited by 44 publications

References 91 publications

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

Distribution of 5-methylcytosine and 5-hydroxymethylcytosine in bovine fetal tissue of the placenta

The role of active DNA demethylation and Tet enzyme function in memory formation and cocaine action

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