Mammalian cytosine methylation at a glance

Abstract

In mammals, methylation at symmetric CpG dinucleotides is necessary for the heritable silencing and regulation of many different classes of DNA sequences. These include highly abundant retrotransposons, such as the long terminal repeat (LTR)-based endogenous retroviruses, [e.g. intercisternal A particles (IAPs)] and non-LTR based elements [e.g. long interspersed nuclear elements (LINEs)]. Tandem repetitive sequences, such as pericentromeric minor and major satellite sequences, are also densely methylated, which is necessary for their stabilization against rearrangements. DNA methylation is also involved in the regulation of genes that are subject to parent-of-origin imprinting and the inactivation of the silent X chromosome in females. These patterns of DNA methylation are established in the germline and are perpetuated with high fidelity throughout the life of the organism. In humans, alterations in genomic methylation patterns are involved in the etiology of imprinting syndromes such as Beckwith-Wiedemann, Prader-Willi and Angelman, and have been implicated in a number of other human conditions including cancer (Feinberg and Tycko, 2004), autoimmune disease (Teitell and Richardson, 2003) and psychiatric disorders (Jiang et al., 2008). Although the DNA methyltransferases that generate 5-methylcytosine are well characterized (for a review, see Goll and Bestor, 2005), the molecular signals responsible for correct targeting during periods of both establishment and maintenance of genomic methylation patterns remain poorly defined. Recent genetic evidence implicates the involvement of adaptors or cofactors that are capable of interacting directly with the methyltransferases themselves, as well as the involvement of nucleosomal components, enzymes that can post-translationally modify histones, and proteins that are involved in the biogenesis of small RNAs.In this article and its accompanying poster, we summarize the known factors involved in the establishment and maintenance of methylation profiles in the mammalian genome. It is probable that the chromatin landscape containing these target sequences is dynamic and can be altered by histone-modifying enzymes and by the exchange of histone variants. The recently identified inverse relationship between the genomic distribution of DNA methylation and the methylation of both histone H3 at lysine 4 (H3K4) and presence of the histone variant H2A.Z suggests an interaction between DNA methylation and chromatin (Meissner et al., 2008; Zilberman et al., 2008). Transcription is also known to affect DNA methylation at both promoter and non-promoter sequences (Han et al., 2001), suggesting that, outside the repetitive regions of the genome where most methylation occurs, local changes in gene activity can impact the methylation machinery. An RNA pathway has been discovered that regulates de novo DNA methylation in mammals and has parallels to RNA-directed DNA methylation (RdDM), (Matzke et al., 2007), which is well documented in plants. However, it remains unclear how the mammalian factors that are involved in this process (such as the Argonaute proteins MIWI2 and MILI and nuage-associated Maelstrom protein) mediate their effects. The large number of factors that have been shown over the last few years to be involved in the establishment or maintenance of genomic methylation patterns means that a more complete understanding of the regulation of genomic methylation patterns might soon be a reality.Over 100 modified nucleosides are found in nucleic acids (most of them in RNA), but mammalian DNA contains only 5-methylcytosine (m5C) and a small amount of 5-hydroxymethylcytosine (5hmC) in certain cell types, which is derived from m5C (Kriaucionis and Heintz, 2009; Tahiliani et al., 2009). Compared with plant genomes, which can encode more than ten DNA methyltransferase genes, mammals have only three enzymatically active DNA methyltransferases.Studies of mice deficient for the enzyme that would eventually become known as DNA methyltransferase 1 (DNMT1) provided insight into the biological function of DNA methylation (Li et al., 1992). Disruption of DNMT1 function results in embryonic lethality and a reduction in global DNA methylation levels to approximately 5% of that found in wild-type mice (Lei et al., 1996). An oocyte-specific isoform, DNMT1o, is required specifically at the eight-cell stage of embryogenesis to maintain methylation patterns at imprinted loci (Howell et al., 2001). DNMT1 has been shown to be active on hemimethylated DNA, which presumably assists the maintenance and methylation activity of DNMT1 (Yoder et al., 1997). However, this preference for hemimethylated DNA alone cannot account for how DNMT1 is correctly targeted. An N-terminal replication-focus-targeting domain is necessary for coordinating DNA methylation and replication (Leonhardt et al., 1992), and this domain has recently been shown to be necessary for the recruitment of DNMT1 to hemimethylated DNA thr