TET and 5hmC in Neurodevelopment and the Adult Brain
M. Fasolino, S.A. Welsh, Z. Zhou
University of Pennsylvania, Philadelphia, PA, United States
DNA methylation at the 5-carbon of cytosine (C) is widely distributed throughout the mammalian genome, with 5% of all C and 85% of all cytosine-phosphate-guanine dinucleotides (CpGs) being methylated (Lister et al., 2013). Such methylation plays an essential role in various biological functions such as the regulation of gene transcription, establishment and maintenance of cellular identity, imprinting, silencing of transposons and repetitive elements, and chromosome X inactivation (Jaenisch & Bird, 2003). Historically, DNA methylation of C was thought to be a stable covalent modification, existing exclusively as 5-methylcytosine (5mC). However, this view was challenged in 2009 when two seminal papers published in parallel described another C modification, 5-hydroxy- methylcytosine (5hmC), which is formed from the oxidation of 5mC (Kriaucionis & Heintz, 2009; Tahiliani et al., 2009). Tahiliani et al. (2009) also described enzymes that were able to convert 5mC to 5hmC, the Ten-eleven translocation family of enzymes, or Tet enzymes. These enzymes were found to be paralogues of the base J binding proteins (JBPs) from the parasite Trypanosoma brucei. However, instead of converting the base thymine to 5-hydroxymethyl-uracil, as JBP enzymes do, Tet enzymes convert 5mC to 5hmC.
Since its rediscovery in 2009, 5hmC has added an important dimension in understanding the epigenetic regulation of neuronal function (Kriaucionis & Heintz, 2009; Penn, Suwalski, O’Riley, Bojanowski, & Yura, 1972; Wyatt & Cohen, 1953).The particular importance of 5hmC in the brain is highlighted by the fact that although global 5mC levels are similar across different tissue types, levels of 5hmC are highly variable, with the highest concentration in the central nervous system (CNS) (Globisch et al., 2010; Kriaucionis & Heintz, 2009; Munzel et al., 2010). Notably, all mature neurons in the CNS are postmitotic, meaning that they no longer divide. Although it was previously known that 5mC could be passively removed through cell division, the discovery ofTet enzymes meant that 5mC could be actively removed via oxidation by Tets to 5hmC, and this removal could occur in postmitotic cells. Furthermore, 5hmC can also be removed, completely reverting the base back to unmodified C. Removal of 5hmC occurs first via
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DNA Modifications in the Brain ISBN 978-0-12-801596-4
Figure 4.1 Cytosine modification cycle. Unmodified cytosine (C) is converted to 5-methylcytosine (5mC) by DNA methyltransferase (DNMT) enzymes DNMT1, DNMT3a, or DNMT3b. 5mC can then be iteratively oxidized by Ten-eleven translocation (Tet) enzymes Tet1, Tet2, or Tet3 to become 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Thymine-DNA glycosylase (TDG) can recognize the bases of 5fC and 5caC and excise them from the DNA, leaving an abasic site. An abasic site triggers the base excision repair pathway (BER), which restores the base to C.
iterative oxidation by the Ten-eleven translocation (TET) family of proteins (TET1, TET2, and TET3, collectively referred to as TETs), which convert 5hmC to 5-formylcytosine (5fC), and subsequently to 5-carboxylcytosine (5caC) (Ito et al., 2011). Finally, 5caC is converted to C by thymine-DNA glycosylase (TDG)-mediated base excision repair (BER) (He et al., 2011) (Fig. 4.1). Therefore, it has been called into question whether 5hmC is a mere transient, uninformative by-product of DNA demethylation or a stable, purposeful epigenetic mark with biological functional significance. Throughout this chapter, we highlight recent findings that have greatly advanced our understanding of the role of 5hmC in brain.