Abstract
Variation in patterns of gene expression can result from modifications in the genome that occur without a change in the sequence of the DNA; such modifications include methylation of cytosine to generate 5-methylcytosine (5mC) resulting in the generation of heritable epimutation and novel epialleles. This type of non-sequence variation is called epigenetics. The enzymes responsible for generation of such DNA modifications in mammals are named DNA methyltransferases (DNMT) including DNMT1, DNMT2 and DNMT3. The later stages of oxidations to these modifications are catalyzed by Ten Eleven Translocation (TET) proteins, which contain catalytic domains belonging to the 2-oxoglutarate dependent dioxygenase family. In various mammalian cells/tissues including embryonic stem cells, cancer cells and brain tissues, it has been confirmed that these proteins are able to induce the stepwise oxidization of 5-methyl cytosine to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and finally 5-carboxylcytosine (5caC). Each stage from initial methylation until the end of the DNA demethylation process is considered as a specific epigenetic mark that may regulate gene expression. This review discusses controversial evidence for the presence of such oxidative products, particularly 5hmC, in various plant species. Whereas some reports suggest no evidence for enzymatic DNA demethylation, other reports suggest that the presence of oxidative products is followed by the active demethylation and indicate the contribution of possible TET-like proteins in the regulation of gene expression in plants. The review also summarizes the results obtained by expressing the human TET conserved catalytic domain in transgenic plants.
Highlights
Methylated cytosine (5-methylcytosine, 5mC) a common epigenetic mark in most eukaryotes, is involved in many biological processes that have been extensively documented
The dynamics of DNA demethylation is the subject of a relevant review [29], which explains that 5fC and/or 5caC are products of Ten Eleven Translocation (TET) iterative oxidation that might be subsequently excised via the Base Excision Repair (BER) pathway [30,31] (Figures 1 and 2)
The presence of more than 130 dioxygenase genes has been reported in the genome of A. thaliana. This superfamily of dioxygenases includes a group of important catalytic enzymes named Prolyl 4-hydroxylases (P4H) that are found in mammals and plants [79]. This group of enzymes in mammals has been well described and divided into two types according to their localization; first, the collagen-type-P4H that are localized in the endoplasmic reticulum and secondly hypoxia-inducible factor (HIF)-P4Hs that are localized in the cytosol [80,81]
Summary
Methylated cytosine (5-methylcytosine, 5mC) a common epigenetic mark in most eukaryotes, is involved in many biological processes that have been extensively documented. A significant enrichment of DNA methylation, consistent with previous studies, was found in heterochromatin and siRNA clusters and has a pivotal role in silencing transposons [5] Another more recent study explained the direct contribution of DNA methylation to the regulation of endogenous gene expression [6]. It has been widely demonstrated that modification of plant genomes by an array of epigenetic marks is involved in the regulation of plant growth and development [5,7] and in imprinting, an important phenomenon found in both plants and animals [8,9,10,11]. The presence of 5mC in the genomes of higher plants is very common and plays several roles including regulation of gene expression that is important in the process of mobilisation and activation of transposable elements in which the high frequency of this epigenetic mark reduces this mobilization. This review was undertaken in order to assess the evidence relating to the possible presence of oxidised derivatives of 5mC with plant genomes, and to consider the hypothesis that plants contain equivalents to the TET-like enzymes present in animals
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