Playing TETris with DNA modifications

Abstract

Methylation of the fifth carbon of cytosine was the first epigenetic modification to be discovered in DNA. Recently, three new DNA modifications have come to light: hydroxymethylcytosine, formylcytosine, and carboxylcytosine, all generated by oxidation of methylcytosine by Ten Eleven Translocation (TET) enzymes. These modifications can initiate full DNA demethylation, but they are also likely to participate, like methylcytosine, in epigenetic signalling per se. A scenario is emerging in which coordinated regulation at multiple levels governs the participation of TETs in a wide range of physiological functions, sometimes via a mechanism unrelated to their enzymatic activity. Although still under construction, a sophisticated picture is rapidly forming where, according to the function to be performed, TETs ensure epigenetic marking to create specific landscapes, and whose improper build-up can lead to diseases such as cancer and neurodegenerative disorders.

Keywords: DNA modifications; TET proteins; epigenetics; human diseases; hydroxymethylation.

Figure 1. Regulation of TETs/methylcytosine oxidation

TET proteins can be regulated at multiple levels, all having a potential impact on global or local methylcytosine oxidation. Small molecules such as 2-hydroxyglutarate (2-HG) or hydrogen peroxide (H₂O₂) inhibit the catalytic activity of TETs while others, such as vitamin C, enhance their activity. Similarly, small microRNAs (miRs) can also affect TET-mediated 5hmC formation by direct downregulation of TET expression. Finally, TETs are connected to and regulated by chromatin related proteins. For example, TET bind the OGT GlcNAc transferase, which can glycosylate and possibly stabilize TETs.

Figure 2. The expanding TET interaction network

Several proteins and catalytically active complexes have been shown to interact with TET enzymes, some having a role in cell reprogramming or differentiation, TET degradation, or in shaping the chromatin landscape by favouring an open or closed chromatin state. Some factors also seem to impact TET function via an indirect mechanism. This is the case for PARP1 and EZH2 (marked with an asterisk). EBF1 is double-marked to emphasize the fact that, although it can play a role in differentiation, the “EBF1-TET” context has been identified in a chondrosarcoma cell line.

Figure 3. The evolving “TETris playground”

A picture is emerging in which TETs build up specific “DNA modification blocks” (hmC, fC, caC) through their coordinated regulation at multiple levels. The following sequence of events can therefore be suggested: (i) Transcription factors will result in (ii) 5hmC, 5fC, and 5caC formation with 5hmC being more abundant in gene bodies. (iii) These modifications can be further bound by various “binders” or “readers” that will either participate in DNA demethylation or translate the epigenetic signal to transcriptional activation or repression. Other active players are transcriptional regulators and small molecules such as vitamin C that directly affect TET activity and hence the deposition of 5hmC, 5fC, and 5caC. These DNA modification blocks, TETs, and TET regulators can assemble in a gene- and/or a cell-state-dependent manner creating precise landscapes which will ultimately affect gene expression.