PHF6 interacts with the nucleosome remodeling and deacetylation (NuRD) complex

J Proteome Res. 2012 Aug 3;11(8):4326-37. doi: 10.1021/pr3004369. Epub 2012 Jul 3.


Mutations in PHF6 are the cause of Börjeson-Forssman-Lehman syndrome (BFLS), an X-linked intellectual disability (XLID) disorder, and both T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML). The PHF6 gene encodes a protein with two plant homeodomain (PHD)-like zinc finger domains. As many PHD-like domains function to target chromatin remodelers to post-translationally modified histones, this suggests a role for PHF6 in chromatin regulation. However, PHD domains are usually found in association with a catalytic domain, a feature that is lacking in PHF6. This distinct domain structure and the minimal information on its cellular function prompted us to perform a proteomic screen to identify PHF6 binding partners. We expressed recombinant Flag-tagged PHF6 in HEK 293T cells for coimmunoprecipitation, and analyzed the purified products by mass spectrometry. We identified proteins involved in ribosome biogenesis, RNA splicing, and chromatin regulation, consistent with PHF6 localization to both the nucleoplasm and nucleolus. Notably, PHF6 copurified with multiple constituents of the nucleosome remodeling and deacetylation (NuRD) complex, including CHD4, HDAC1, and RBBP4. We demonstrate that this PHF6-NuRD complex is not present in the nucleolus but is restricted to the nucleoplasm. The association with NuRD represents the first known interaction for PHF6 and implicates it in chromatin regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Carrier Proteins / genetics
  • Carrier Proteins / isolation & purification
  • Carrier Proteins / metabolism*
  • Cell Nucleolus / metabolism
  • Conserved Sequence
  • Gene Expression
  • Gene Expression Regulation
  • HEK293 Cells
  • Histone Deacetylase 1 / isolation & purification
  • Histone Deacetylase 1 / metabolism
  • Humans
  • Immunoprecipitation
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex / isolation & purification
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex / metabolism*
  • Protein Interaction Domains and Motifs
  • Protein Interaction Mapping
  • Repressor Proteins / isolation & purification
  • Repressor Proteins / metabolism
  • Sin3 Histone Deacetylase and Corepressor Complex


  • Carrier Proteins
  • PHF6 protein, human
  • Repressor Proteins
  • SIN3A transcription factor
  • HDAC1 protein, human
  • Histone Deacetylase 1
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex
  • Sin3 Histone Deacetylase and Corepressor Complex