The A, B, Gs of silencing.

Transcriptional silencing of mammalian genes is mediated by at least two modes of methylation: (1) cytosine methylation of DNA, and (2) methylation of the histones tails—both of which play an important role in transcriptional silencing from chromosomal DNA. Although there is some evidence that these pathways are interdependent, experimentally, they have largely been treated as two distinct processes. In this issue of Genes & Development, Smallwood et al. (2007) have taken a pioneering step toward defining the molecular mechanism by which these two types of methylations can cooperate to silence a euchromatic gene, and demonstrate that the DNA methyltransferase 1 (DNMT1) cytosine methyltransferase physically and functionally interacts with three Heterochromatin Protein 1 (HP1) family members ( , , and ) to implement gene silencing. DNA methylation is required for normal development in mammals. It is brought about by the de novo methyltransferases DNMT3a and DNMT3b and is propagated by the maintenance methyltransferase DNMT1 (for review, see Goll and Bestor 2005). DNA methylation is associated with silencing repetitive elements in the genome, X-chromosome inactivation in female mammals, and silencing of individual genes during development (for review, see Li and Bird 2007). Furthermore, DNA methylation is misregulated in cancer cells such that tumor suppressor genes are silenced to favor the growth of the tumor while repetitive regions of the genome are desilenced, which can contribute to genomic instability (for review, see Baylin and Jones 2007). However, the exact molecular mechanism of DNA methylation in transcriptional regulation and during the pathogenesis of cancer remains unclear. The core histone proteins are wrapped by 147 base pairs of DNA forming the intact nucleosome. The histone N termini, or tails, extend away from the core of the nucleosome and are available for interactions with the DNA, histone-modifying enzymes, and other proteins, which alter the nucleosome structure (Shilatifard 2006). There are multiple modification sites on each histone tail, and some amino acids in the histone tail can be modified in two or more ways. Histone methylation at Lys 9 of H3 is associated with silencing at both heterochromatin and euchromatic sequences in a variety of systems (for review, see Ebert et al. 2006; Shilatifard 2006). Recent evidence demonstrates that it is also associated with transcribed regions of euchromatic genes, indicating that this modification can have distinct meanings in different contexts (Vakoc et al. 2005; Eissenberg and Shilatifard 2006). Not only can the lysine residues within histones be modified by methylation, this modification can occur in three different states. Lysine residues can accept up to three methyl groups and therefore be mono-, di-, or trimethylated. For H3K9, the pattern of mono-, di-, and trimethylation is mediated by the catalytic properties of different enzymes. For example, the G9a methyltransferase mediates dimethylation of H3K9 and is associated with silencing of euchromatic genes (Tachibana et al. 2002; Peters et al. 2003). Not only can G9a regulate the pattern of H3K9 methylation, it also functions in some way in regulating DNA methylation at multiple sites (Xin et al. 2003; Feldman et al. 2006). Furthermore, it has been demonstrated in Arabidopsis that loss of DNA methyltransferase activity can result in alteration in H3K9 methylation patterns (Soppe et al. 2002). The attachment of methyl groups to histone proteins occurs predominantly at specific lysine or arginine residues, and each site requires the enzymatic activity of a specific class of enzymes. Furthermore, methylated lysine residues within histones can serve as a specific binding site for different proteins. For example, HP1 can recognize and bind to diand trimethylated H3K9 via its chromodomain (Bannister et al. 2001; Lachner et al. 2001). HP1 was first characterized in Drosophila as a nonhistone chromosomal protein that localized to heterochromatin and was required for gene silencing (Eissenberg and Elgin 2000). Both flies and mammals have more than one HP1-like protein, with each having distinct localizations (for review, see Hediger and Gasser 2006). Mammals have three HP1 isoforms: HP1 , HP1 , and HP1 . HP1 localizes primarily to pericentric heterochromatin, HP1 localizes primarily to promoters of silent euchromatic genes, and HP1 localizes primarily to coding regions of transcribed genes (Hediger and Gasser 2006). The basis for this localization is unknown, but in Drosophila it appears to depend, in part, on the hinge region and chromo shadow domain of each protein (Smothers and Henikoff 2001). Diversification of function of different HP1s could explain the recent finding of Blobel and colleagues (Vakoc et al. 2005) that H3K9 methylation is found in the coding regions of actively Corrresponding author. E-MAIL ASH@Stowers-Institute.org; FAX (816) 926-4112. Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.1559407.