Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity

Abstract

Polycomb-group proteins are transcriptional repressors with essential roles in embryonic development. Polycomb repressive complex 2 (PRC2) contains the methyltransferase activity for Lys27. However, the role of other histone modifications in regulating PRC2 activity is just beginning to be understood. Here we show that direct recognition of methylated histone H3 Lys36 (H3K36me), a mark associated with activation, by the PRC2 subunit Phf19 is required for the full enzymatic activity of the PRC2 complex. Using NMR spectroscopy, we provide structural evidence for this interaction. Furthermore, we show that Phf19 binds to a subset of PRC2 targets in mouse embryonic stem cells and that this is required for their repression and for H3K27me3 deposition. These findings show that the interaction of Phf19 with H3K36me2 and H3K36me3 is essential for PRC2 complex activity and for proper regulation of gene repression in embryonic stem cells.

Polycomb-like proteins link the PRC2 complex to CpG islands

“…3a, b), similar to the results from isolated Tudor domains 4,6,7,11,15,16 , suggesting that the presence of the other domains does not interfere with the histone binding preference. In addition, we confirmed that the Tudor domains rather than the PHD1/2 fingers are responsible for the above recognition, as mutation of an aromatic-cage residue in the Tudor domain (Y47A for PHF1, Y62A for MTF2) led to a complete loss in binding affinity (Extended Data Table 2).…”

“…Polycomb-like proteins (PCLs), including PHF1, MTF2 and PHF19, are PRC2 associated factors that form sub-complexes with PRC2 core components 3 , and have been proposed to modulate PRC2’s enzymatic activity or its recruitment to specific genomic loci 4–13 . Mammalian PRC2 binding sites are enriched in CG content, which correlate with CpG islands that display a low level of DNA methylation 14 .…”

“…PHF1, MTF2 and PHF19 (also known as PCL1, PCL2 and PCL3, respectively) are mammalian Polycomb-like proteins that directly interact with PRC2 4,5 . They all possess a Tudor domain, two PHD fingers, an extended homologous region clustered at the N-terminus, and a chromo-like domain located at the C-terminus (Fig.…”

“…1a). Currently, only the structures of the isolated Tudor domains of PCLs have been solved, which bind preferentially to histone H3 trimethylated at lysine 36 (H3K36me3) 4,6,7,11,15,16 . We solved the crystal structure of the PHF1 Tudor-PHD1-PHD2-EH cassette at 1.9 Å resolution (Extended Data Table 1).…”

“…PCL proteins have been proposed to be involved in recruiting PRC2 to chromatin 4,6,10,12,24 . Analysis of publically available data 10,12 demonstrated that MTF2 and PHF19 colocalize with PRC2 at a subset of unmethylated CpG island-containing promoters in mouse embryonic stem cells (mESCs, Fig.…”