The SUVR4 Histone Lysine Methyltransferase Binds Ubiquitin and Converts H3K9me1 to H3K9me3 on Transposon Chromatin in Arabidopsis

摘要

Chromatin structure and gene expression are regulated by posttranslational modifications (PTMs) on the N-terminal tails of histones. Mono-, di-, or trimethylation of lysine residues by histone lysine methyltransferases (HKMTases) can have activating or repressive functions depending on the position and context of the modified lysine. In Arabidopsis, trimethylation of lysine 9 on histone H3 (H3K9me3) is mainly associated with euchromatin and transcribed genes, although low levels of this mark are also detected at transposons and repeat sequences. Besides the evolutionarily conserved SET domain which is responsible for enzyme activity, most HKMTases also contain additional domains which enable them to respond to other PTMs or cellular signals. Here we show that the N-terminal WIYLD domain of the Arabidopsis SUVR4 HKMTase binds ubiquitin and that the SUVR4 product specificity shifts from di- to trimethylation in the presence of free ubiquitin, enabling conversion of H3K9me1 to H3K9me3 in vitro . Chromatin immunoprecipitation and immunocytological analysis showed that SUVR4 in vivo specifically converts H3K9me1 to H3K9me3 at transposons and pseudogenes and has a locus-specific repressive effect on the expression of such elements. Bisulfite sequencing indicates that this repression involves both DNA methylation–dependent and –independent mechanisms. Transcribed genes with high endogenous levels of H3K4me3, H3K9me3, and H2Bub1, but low H3K9me1, are generally unaffected by SUVR4 activity. Our results imply that SUVR4 is involved in the epigenetic defense mechanism by trimethylating H3K9 to suppress potentially harmful transposon activity. Author Summary The characteristics of the diverse cell types in multicellular organisms result from differential gene expression that is dependent on the level of DNA packaging. Genes that are essential for the function of the cell are expressed; while unessential genes, and DNA elements (transposons or “jumping genes”) that can move from one position to another within a genome and potentially cause deleterious mutations, are repressed. The mechanisms evolved in eukaryotes to avoid unwanted gene expression and transposon movement include DNA methylation and specific combinations of post translational modifications (PTMs) of the histones that package DNA. Here we show that the SUVR4 enzyme binds the signaling protein ubiquitin and that ubiquitin enables the enzyme to trimethylate lysine 9 (H3K9me3) of histone H3. In contrast to other reports demonstrating an activating role on expressed genes, we show that H3K9me3 has a locus-specific repressive effect on the expression of transposons. The specificity is maintained by the communication with other PTMs on transposons and euchromatic genes, which has a stimulating or repressing effect on enzyme activity, respectively. Our results demonstrate how repression of transcription can be restricted to specific targets and demonstrate that this repression involves a context-dependent read-out of different PTMs.