DNA methylation, its mediators and genome integrity

Abstract

DNA methylation regulates many cellular processes, including embryonic development, transcription, chromatin structure, X-chromosome inactivation, genomic imprinting and chromosome stability. DNA methyltransferases establish and maintain the presence of 5-methylcytosine (5mC), and ten-eleven translocation cytosine dioxygenases (TETs) oxidise 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), which can be removed by base excision repair (BER) proteins. Multiple forms of DNA methylation are recognised by methyl-CpG binding proteins (MeCPs), which play vital roles in chromatin-based transcriptional regulation, DNA repair and replication. Accordingly, defects in DNA methylation and its mediators may cause silencing of tumour suppressor genes and misregulation of multiple cell cycles, DNA repair and chromosome stability genes, and hence contribute to genome instability in various human diseases, including cancer. Thus, understanding functional genetic mutations and aberrant expression of these DNA methylation mediators is critical to deciphering the crosstalk between concurrent genetic and epigenetic alterations in specific cancer types and to the development of new therapeutic strategies.

Keywords: BRCA1; DNA glycosylases; DNA methylation; DNA methyltransferases; genome instability.; methyl-CpG binding proteins.

Figure 1

Major forms and distribution of DNA methylation. (A) The three major forms of cytosine bases in mammalian DNA. The 5-position of cytosine is covalently methylated by DNA cytosine methyltransferases (DNMTs) with the presence of co-factor S-adenosyl methionine (SAM). The resulting 5-methylcytosine (5mC) is mostly found on CpG dinucleotides in somatic cells. 5-hydroxymethylcytosine (5hmC) is formed by methylation and subsequent hydroxylation and is mediated by the ten-eleven translocation cytosine dioxygenases (TETs). (B) Distribution of CpG dinucleotides in mammalian genomes. In vertebrate genomes, CpG dinucleotides are generally highly methylated, whereas CpG islands (CGIs) that are associated with gene promoters have exceptional global unmethylated patterns. Exceptions include CGIs on inactive X-chromosomes in female cells, where CGIs are hypermethylated. In addition to canonical CGIs located at annotated transcription start sites (TSSs), orphan CGIs of unknown function are found within gene bodies (intragenic) and between annotated genes (intergenic). Unmethylated CGIs at 5' ends of multiple genes are positively correlated with transcriptional activity (active, left), whereas a small number of genes are hypermethylated at their promoter CGIs and are repressed in specific cell types (inactive, right). Gene bodies are often methylated with higher DNA methylation at exons than introns, and 5hmC is present at expressed gene bodies and are the proposed 5mC oxidation products of TET enzymes (labelled white squares at body of gene). White circles, nonmethylated CpGs; black circles, methylated CpGs; white squares, hydroxylmethylated CpGs; red boxes, active and transcribed exons; black boxes, inactive and silenced exons; transcriptional states of these genes are represented by the red arrow (active) and the black cross (inactive).

Figure 2

Mediators of DNA methylation machinery. (A) Domain structures of mammalian DNA methyltransferases (DNMTs). Functional domains in the N-terminal regions of DNMTs are shown and the conserved motifs in the C-terminal region are labelled. In the N-terminal region, the sub-domains include a proliferating cell nuclear antigen binding site (PBD), nuclear localisation signal region (NLS), plant homeo domain (PHD) like domain and PWWP domain (highly conserved proline-tryptophan-tryptophan-proline motif that is involved in protein-protein interactions) and bromo-adjacent homology domains (BAH). N- and C-terminal domains are linked by Gly-Lys dipeptides. Highly conserved C-terminal methyltransferase motifs are shown as thick black lines (indicated as I-X). (B) Domain structures of methyl-CpG binding proteins (MeCPs). Three families of characterised mammalian MeCPs include (1) the methyl-CpG binding domain proteins (MBDs) MBD1, MBD2, MBD3, MBD4 and MeCP2. (2) the structurally unrelated methyl-CpG binding zinc-finger proteins of the Kaiso family KAISO/ZBTB33, ZBTB4 and ZBTB38 and (3) the methyl-CpG binding SRA domain proteins of the UHRF family UHRF1 and its homologue UHRF2. Labelled sub-domains include MBD, methyl-CpG binding domain; TRD, trans-repressor domain; GR, E, P, amino acid repeats; BTB/POZ, broad complex, tramtrack, and bric à brac domains; ZF, zinc finger motifs; UBL, ubiquitin-like motif; PHD, Plant homeodomain and SRA, SET and Ring-associated domain. DNA binding regions are indicated. (C) Domain structures of ten-eleven translocation methylcytosine dioxygenases (TETs). Schematic representation of conserved domains of mouse Tet proteins is shown, including a double-stranded-helix (DSBH) fold (all Tets), cysteine-rich (Cys-rich) domain (all Tets) and CXXC zinc fingers (Tet1 and Tet3).