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Abstract
PR-Set7/Set8/KMT5a is the sole histone H4 lysine 20 monomethyltransferase (H4K20me1) in metazoans and is essential for proper cell division and genomic stability. We unexpectedly discovered that normal cellular levels of monomethylated histone H3 lysine 9 (H3K9me1) were also dependent on PR-Set7, but independent of its catalytic activity. This observation suggested that PR-Set7 interacts with an H3K9 monomethyltransferase to establish the previously reported H4K20me1-H3K9me1 trans-tail ‘histone code’. Here we show that PR-Set7 specifically and directly binds the C-terminus of the Riz1/PRDM2/KMT8 tumor suppressor and demonstrate that the N-terminal PR/SET domain of Riz1 preferentially monomethylates H3K9. The PR-Set7 binding domain was required for Riz1 nuclear localization and maintenance of the H4K20me1-H3K9me1 trans-tail ‘histone code’. Although Riz1 can function as a repressor, Riz1/H3K9me1 was dispensable for the repression of genes regulated by PR-Set7/H4K20me1. Frameshift mutations resulting in a truncated Riz1 incapable of binding PR-Set7 occur frequently in various aggressive cancers. In these cancer cells, expression of wild-type Riz1 restored tumor suppression by decreasing proliferation and increasing apoptosis. These phenotypes were not observed in cells expressing either the Riz1 PR/SET domain or PR-Set7 binding domain indicating that Riz1 methyltransferase activity and PR-Set7 binding domain are both essential for Riz1 tumor suppressor function.
Highlights
Compaction of the large eukaryotic genome in the small volume of the nucleus is facilitated by the formation of chromatin, a structure composed mainly of DNA and the canonical histone proteins
Cellular H3K9me1 levels are not dependent on PR-Set7 enzymatic activity, as ectopic expression of a dominant negative PR-Set7 catalytically dead point mutant significantly reduced global H4K20me1 but not H3K9me1 (Figure 1A, Supplementary Figure S1). These findings strongly suggested that PR-Set7 interacts with an unknown H3K9 monomethyltransferase and that this interaction is required for a significant portion of H3K9me1 in human cells
Consistent with this, cells expressing GAL4-DBDPR-Set7 and FLAG-Riz1 C-terminus (Riz1C), which likely competitively inhibits binding of endogenous Riz1 to PR-Set7 (Figure 3C), resulted in the ablation of H3K9me1 at the transgene. These results demonstrate that PR-Set7 is sufficient for Riz1 recruitment and establishment of the H4K20me1-H3K9me1 trans-tail ‘histone code’ at an ectopic locus and that Riz1 recruitment to chromatin is mediated by the PR-Set7 binding domain
Summary
Compaction of the large eukaryotic genome in the small volume of the nucleus is facilitated by the formation of chromatin, a structure composed mainly of DNA and the canonical histone proteins. In addition to genome compaction, histones directly participate in the regulation of essential DNA-templated processes including transcription, replication and repair. Increasing evidence supports the ‘histone code’ hypothesis where a single or specific combination of histone posttranslational modifications functions to establish and maintain the associated DNA-templated process at certain genomic loci [1]. The concurrent H3K4me and H3K27me modifications at promoters of developmentally regulated genes are associated with their transcriptionally ‘poised’ state in embryonic stem cells [2]. During differentiation, these modifications separately resolve such that promoters of activated genes have only H3K4me, whereas promoters of repressed genes have only H3K27me
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