PHF8, H3K4me3, control IgG / input DNA ChIP-seq in HeLa, 293T and Hs68
PHF8 targets histone methylation and RNA polymerase II to activate transcription.
Mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 contains a plant homeodomain (PHD) in its N-terminus and is member of a family of JmjC-domain containing proteins. While PHDs can act as methyl lysine recognition motifs, JmjC-domains can catalyze lysine demethylation. Here, we show that PHF8 is a histone demethylase that removes repressive histone H3 dimethyl lysine 9 marks. Our biochemical analysis revealed specific association of the PHF8 PHD domain with histone H3 trimethylated at lysine 4 (H3K4me3). Chromatin-immunoprecipitation followed by high throughput sequencing indicated that PHF8 is enriched at transcription start sites of many active or poised genes, mirroring the presence of RNA polymerase II (RNAPII) and of H3K4me3-bearing nucleosomes. We show that PHF8 can act as a transcriptional co-activator and its activation function largely depends on binding of the PHD to H3K4me3. Furthermore, we present evidence for direct interaction of PHF8 with the C-terminal domain of RNAPII. Importantly, a PHF8 disease mutant is defective in demethylation and in co-activation. This is the first demonstration of a chromatin-modifying enzyme, which associates with promoters via the H3K4me3 modification and RNAPII.