DNA methylation and hydroxymethylation in stem cells

Abstract

In mammals, DNA methylation and hydroxymethylation are specific epigenetic mechanisms that can contribute to the regulation of gene expression and cellular functions. DNA methylation is important for the function of embryonic stem cells and adult stem cells (such as haematopoietic stem cells, neural stem cells and germline stem cells), and changes in DNA methylation patterns are essential for successful nuclear reprogramming. In the past several years, the rediscovery of hydroxymethylation and the TET enzymes expanded our insights tremendously and uncovered more dynamic aspects of cytosine methylation regulation. Here, we review the current knowledge and highlight the most recent advances in DNA methylation and hydroxymethylation in embryonic stem cells, induced pluripotent stem cells and several well-studied adult stems cells. Our current understanding of stem cell epigenetics and new advances in the field will undoubtedly stimulate further clinical applications of regenerative medicine in the future.

Keywords: adult stem cells; epigenetics; hydroxymethylation; methylation; stem cells.

Figure 1

Hydroxymethylcytosine (hmC)-dependent DNA demethylation pathway. Cytosines (C) that are methylated to methylcytosine (mC) by DNA methyltransferases (DNMTs) can be converted to hmC by TET enzymes (TETs). Subsequently, hmC can be oxidized to formylcytosine (fC) and carboxylcytosine (caC) by TETs or deaminated to hydroxymethyluracil (hmU) by activation-induced deaminase/apolipoprotein B mRNA-editing enzyme complex (AID/APOBEC). These products can then be excised by thymine DNA glycosylase (TDG) with or without SMUG1, followed by base excision repair (BER). DNMT3 may contribute to DNA demethylation by dehydroxymethylation, but further experiments are needed to confirm this pathway. In addition, thymine (T) is also severed as a substrate of TETs and can be catalysed to hmU.

Figure 2

Roles of DNMTs and TET2 in regulating haematopoietic stem cell (HSC) self-renewal and differentiation. (a) HSCs are derived from conditional knockout (KO) mice. Loss of DNMT1 results in the inhibition of HSC self-renewal. Reduced DNMT1 activity leads to DNA hypomethylation in the promoters of the myeloerythroid progenitor regulators and causes preferential differentiation from HSCs into myeloerythroid progeny (MP), rather than lymphoid progeny (LP). (b) Conditional KO of Dnmt3a in the haematopoietic compartment increases HSC numbers and impairs HSC differentiation, while double KO of Dnmt3a and Dnmt3b in HSCs leads to a more severe arrest of HSC differentiation. Alternatively, Dnmt3b^−/− HSCs show a mild in vivo phenotype, indicating that DNMT3a can compensate for the vast majority of DNMT3b loss. (c) Under normal conditions, TET2 suppresses HSC self-renewal and myeloid malignancies; it is highly involved in DNA demethylation and contributes to balancing the critical threshold of DNA methylation status. Loss of TET2 function, usually caused by mutation or deletion, results in the dysregulation of DNA methylation, increased self-renewal and aberrant differentiation of HSCs and initiates myeloproliferative disorders.