Active DNA demethylation: many roads lead to Rome

An Erratum to this article was published on 08 September 2010

Key Points

  • In mammals and plants, DNA methylation refers to the addition of a methyl group to the fifth carbon of base C. Active DNA demethylation involves the enzymatic replacement of 5-methylcytosine (5meC) with C.

  • Global DNA demethylation has only been seen during early development in the zygotic paternal pronuclei and in primordial germ cells. However, imprinted genes are protected from demethylation in the zygote.

  • Loci-specific active DNA demethylation has been seen in somatic cells such as post-mitotic neurons and is important for the expression of neurogenesis genes. Recent studies have also indicated that nuclear hormone target promoters experience periodic methylation and demethylation that correlates with nuclear receptor binding and target gene expression.

  • In plants, biochemical and genetic evidence support the notion that DNA demethylation is achieved through base excision repair (BER) initiated by the Demeter (Dme) family of 5meC glycosylases. It is unlikely that mammals use a similar mechanism as the mammalian glycosylases T DNA glycosylase (TDG) and methyl-CpG-binding domain protein 4 (MBD4) possess weak excision activity against 5meC compared to T.

  • In contrast to the direct excision of 5meC, meC may first be deaminated to generate T and the resulting mismatch can initiate BER. Studies in zebrafish embryos have supported such a cooperative model, whereby deamination of 5meC can be carried out by activation-induced deaminase (AID), and T•G mismatch is repaired by MBD4.

  • The ten-eleven translocation (TET) family of proteins can hydroxylate 5meC to generate 5-hydroxymethylcytosine (5hmC), a modification that is present in embryonic stem (ES) cells and Purkinje neurons. The functional consequences and fate of 5hmC are unclear. However, TET1 plays a crucial role in ES cell identity as knockdown of TET1 results in defects in ES cell self-renewal and maintenance.

  • Recent studies have established a role for the elongator complex in zygotic paternal pronuclei demethylation as knockdown of the elongator components elongator complex protein 1 (ELP1), ELP3 and ELP4 impairs paternal genome demethylation. Although direct biochemical evidence is currently lacking, the radical SAM domain of ELP3 seems to be involved in the demethylation process.

  • Because promoter methylation of tumour suppressor genes has been implicated in cancer, understanding the mechanisms of DNA demethylation will facilitate the development of novel therapies. In addition, identification of the DNA demethylases also has implications in somatic cell reprogramming as promoter demethylation of pluripotent genes is crucial for this process.

Abstract

DNA methylation is one of the best-characterized epigenetic modifications and has been implicated in numerous biological processes, including transposable element silencing, genomic imprinting and X chromosome inactivation. Compared with other epigenetic modifications, DNA methylation is thought to be relatively stable. Despite its role in long-term silencing, DNA methylation is more dynamic than originally thought as active DNA demethylation has been observed during specific stages of development. In the past decade, many enzymes have been proposed to carry out active DNA demethylation and growing evidence suggests that, depending on the context, this process may be achieved by multiple mechanisms. Insight into how DNA methylation is dynamically regulated will broaden our understanding of epigenetic regulation and have great implications in somatic cell reprogramming and regenerative medicine.

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Figure 1: Mechanisms of DNA methylation and demethylation.
Figure 2: Dynamics of DNA methylation during development.
Figure 3: Locus-specific active DNA demethylation in somatic cells.
Figure 4: Base excision repair-based mechanisms for DNA demethylation.
Figure 5: Oxidative demethylation by TET proteins.
Figure 6: Proposed mechanism for ELP3-mediated DNA demethylation.

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Acknowledgements

We thank S. J. Booker for discussions regarding the radical SAM mechanism, and K. Hong and A. D'Alessio for critical comments on the manuscript. We apologize to colleagues whose work cannot be cited owing to space constraints. Work in the Zhang laboratory is supported by the National Institutes of Health (GM68804) and the Howard Hughes Medical Institute, of which Y.Z. is an investigator.

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Glossary

Imprinted gene

A gene that is expressed in a parent-of-origin-specific manner.

Inactive X chromosome

The copy of X chromosome that is silenced in female chromosomes in order to equalize the expression of genes located in the X chromosome in males and females.

DNA methyltransferase

An enzyme that catalyses the addition of a methyl group to C or A.

Hemi-methylated DNA

Duplex DNA in which only one of the two strands is methylated.

Zona pellucida

The glycoprotein coat that surrounds the oocytes and the early embryos of mammals.

Polar body

The structure that is extruded from the oocyte during meiosis and contains one haploid set of chromosomes.

Parthenogenesis

The production of a diploid offspring from two sets of haploid maternal gametes and no paternal contribution.

Gynogenesis

Parthenogenesis in which the embryo contains only maternal chromosomes owing to the failure of the sperm to fuse with the egg nucleus.

Digynic triploid

An embryo that contains two maternal genomes and one paternal genome.

Bisulphite sequencing

A technique in which the treatment of DNA with bisulphite, which converts C to U but does not modify meC, is used to determine the DNA methylation pattern.

Blastocyst

An embryonic stage that is characterized by the formation of the first definitive lineages.

Primordial germ cell

One of a population of embryonic cells from which germ cells are formed.

RNA editing

The post-transcriptional modification of RNA primary sequence by the insertion and/or deletion of specific bases, or the chemical modification of adenosine to inosine or cytidine to uridine.

Somatic hypermutation

The mutation of the immunoglobulin variable region in mature B cells during an immune response. It results in affinity maturation of the antibody response. Like class switch recombination, it requires activation-induced cytidine deaminase.

Class switch recombination

A mechanism that changes the class or isotype of antibody produced by an activated B cell. This does not change the affinity towards an antigen, but instead allows for interaction with different effector molecules.

JmjC

(Jumonji C). An evolutionarily conserved motif. Proteins containing this domain are predicted to be protein hydroxylases or histone demethylases.

Base J-binding protein

A protein that binds to base J (β-D-glucosylhydroxymethyl-U), a modified T produced by hydroxylation and glucosylation of the methyl group of T.

Elongator complex

A protein complex originally identified in budding yeast to be associated with the elongating and hyperphosphorylated RNA polymerase II. It has also been implicated in tRNA modification, exocytosis and neuronal maturation.

SAM domain

A protein domain containing an Fe–S cluster that uses S-adenosylmethionine (SAM) to catalyse various radical reactions.

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Wu, S., Zhang, Y. Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 11, 607–620 (2010). https://doi.org/10.1038/nrm2950

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