PHF8 targets histone methylation and RNA polymerase II to activate transcription

Mol Cell Biol. 2010 Jul;30(13):3286-98. doi: 10.1128/MCB.01520-09. Epub 2010 Apr 26.

Abstract

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 a 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 with histone H3 trimethylated at lysine 4 (H3K4me3). Chromatin immunoprecipitation followed by high-throughput sequencing indicated that PHF8 is enriched at the 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 coactivator and that 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 was defective in demethylation and in coactivation. This is the first demonstration of a chromatin-modifying enzyme that is globally recruited to promoters through its association with H3K4me3 and RNAPII.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Cell Line
  • Gene Expression Profiling
  • Gene Knockdown Techniques
  • Histone Demethylases / genetics
  • Histone Demethylases / metabolism*
  • Histones / metabolism*
  • Humans
  • Lysine / metabolism
  • Methylation
  • Microarray Analysis
  • Molecular Sequence Data
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism*
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*

Substances

  • Histones
  • Recombinant Fusion Proteins
  • Transcription Factors
  • Histone Demethylases
  • PHF8 protein, human
  • RNA Polymerase II
  • Lysine