Relationship between Histone H3 Lysine 9 Methylation, Transcription Repression, and Heterochromatin Protein 1 Recruitment

Histone H3 lysine 9 (H3-K9) methylation has been shown to correlate with transcriptional repression and serve as a specific binding site for heterochromatin protein 1 (HP1). In this study, we investigated the relationship between H3-K9 methylation, transcriptional repression, and HP1 recruitment by comparing the effects of tethering two H3-K9-specific histone methyltransferases, SUV39H1 and G9a, to chromatin on transcription and HP1 recruitment. Although both SUV39H1 and G9a induced H3-K9 methylation and repressed transcription, only SUV39H1 was able to recruit HP1 to chromatin. Targeting HP1 to chromatin required not only K9 methylation but also a direct protein-protein interaction between SUV39H1 and HP1. Targeting methyl-K9 or a HP1-interacting region of SUV39H1 alone to chromatin was not sufficient to recruit HP1. We also demonstrate that methyl-K9 can suppress transcription independently of HP1 through a mechanism involving histone deacetylation. In an effort to understand how H3-K9 methylation led to histone deacetylation in both H3 and H4, we found that H3-K9 methylation inhibited histone acetylation by p300 but not its association with chromatin. Collectively, these data indicate that H3-K9 methylation alone can suppress transcription but is insufficient for HP1 recruitment in the context of chromatin exemplifying the importance of chromatin-associated factors in reading the histone code. In eukaryotic cells, DNA is tightly associated with histones and other factors to form chromatin. The nucleosome is the basic building block of chromatin and consists of approximately 150 bp of DNA coiled around an octamer of histones. The histone octamer contains two copies of each of the core histones, H2A, H2B, H3, and H4. The N-terminal region of each core histone is unstructured when crystallized and therefore is likely to be a highly dynamic structure. These histone tails protrude out from the globular center of the nucleosome where they may interact with nuclear factors. The N-terminal tails are subject to a variety of posttranslational modifications, including phosphorylation, acetylation, methylation, and ubiquitylation. These modifications affect the binding of proteins to the histone tails and thus regulate the nature of the protein complexes that will associate with a region of chromatin. The ability of proteins to specifically associate with certain histone modifications is the basis of the histone code theory (15, 48). According to this theory, specific proteins will associate with histone tails containing certain modifications. These proteins may function to activate or inhibit transcription or serve to maintain a specific chromatin structure. The best-studied histone modifications are acetylation and methylation. Histone acetylation is generally associated with regions of active transcription. Many transcriptional coactivators contain histone acetyltransferase (HAT) activity, including CBP/p300 (3, 35), the p160 family (46), and P/CAF (63). While arginine methylation of H3 and H4 is associated with transcriptional activation, lysine methylation of histones may have positive or negative effects on transcription, depending on the methylation site(s) (18). Methylation of H3-K9 and H3-K27 is generally associated with repression, whereas methylation of H3-K4, -K36, and -K79 has been implicated in the transcriptional activation process (19, 30, 34, 43, 60). Indeed, the arginine methyltransferases, coactivator-associated arginine methyltransferase 1 (5) and PRMT1 (17), are transcriptional coactivators, while H3-K9 methyltransferases, such as SUV39H1 and G9a (10, 40, 43, 50, 52), are repressors.