5hmC: roles for the ‘6th DNA base’ in development and cancer?

Posted by Biome on 15th May 2013 - 0 Comments

5-hydroxymethylcytosine (5hmC) is a stable DNA base that appears regularly in the mammalian genome, yet its function remains elusive. A recent review in Epigenetics & Chromatin by Gerd Pfeifer and colleagues (Beckman Research Institute, California) provides a forward-looking overview of current evidence on the possible roles of 5hmC in development and cancer. This article is part of a special series, which marks the 2013 BioMed Central ‘Epigenetics & Chromatin: Interactions and Processes’ conference, and aims to discuss how epigenetic processes and chromatin components together regulate cellular processes.

Several years ago it was discovered that epigenetic modifications to cytosine can translate to altogether different functions. 5-methylcytosine (5mC), commonly referred to as the ‘5th DNA base’, is oxidised by the TET family of enzymes to form 5hmC – unsurprisingly known as the ‘6th DNA base’. Pfeifer and colleagues discuss the dual role of 5hmC as a DNA base and as an intermediate in DNA demethylation.

DNA Methyltransferase 1 on DNA. Image source: RSCB PDB

DNA Methyltransferase 1 (blue) bound to DNA (red). Image source: RSCB PDB

During DNA demethylation, when 5mC reverts back to cytosine through the action of DNA methyltransferase (DNMT1), it is proposed that 5mc must first transition to 5hmC. The level of 5hmC varies significantly between different tissue types in mammals, with many tissues accumulating much more than would be expected if it was just a transient state in the process of DNA demethylation. Evidence suggests that 5hmC also functions as a stable nucleotide base with unique biochemical properties.

To probe what 5hmC is up to, several studies have examined the effects of deleting the enzymes responsible for its production. The progeny of Tet1 and Tet2 knockout mice, for example, have been shown to exhibit deficiencies in DNA demethylation, with the majority dying during embryogenesis. Further analysis of 5hmC in mammalian primordial germ cells, using techniques such as TAB-sequencing, is needed to uncover how important its formation may be during global DNA demethylation. Given the abundance of 5hmC in brain tissue, it is also thought likely that this base is involved in neuronal development.

Looking to cancer for further insights into 5hmC function reveals a significant reduction in 5hmC levels in tumours when compared to surrounding normal tissue. Pfeifer and colleagues have themselves demonstrated the loss of 5hmC in several types of cancers. Studies suggest that this base cannot be maintained in proliferating cells – a finding that may aid in understanding the mechanism behind cancer-associated DNA hypermethylation and more practically may prove useful in the early diagnosis of malignancy.

Current knowledge on the exact functions of 5hmC, particularly in development and cancer, is still in its infancy, and it is clear that more evidence is required to support the proposed roles. However, emerging data summarised in this review is encouraging and provides important details on the relatively recently established ‘6th DNA base’.



5-hydroxymethylcytosine and its potential roles in development and cancer

Pfeifer GP, Kadam S and Jin SG
Epigenetics & Chromatin 2013, 6:10 (01/05/2013)

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