Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27

Genes Dev. 2004 Jul 1;18(13):1592-605. doi: 10.1101/gad.1200204.

Abstract

Polycomb group (PcG) complexes 2 and 3 are involved in transcriptional silencing. These complexes contain a histone lysine methyltransferase (HKMT) activity that targets different lysine residues on histones H1 or H3 in vitro. However, it is not known if these histones are methylation targets in vivo because the human PRC2/3 complexes have not been studied in the context of a natural promoter because of the lack of known target genes. Here we report the use of RNA expression arrays and CpG-island DNA arrays to identify and characterize human PRC2/3 target genes. Using oligonucleotide arrays, we first identified a cohort of genes whose expression changes upon siRNA-mediated removal of Suz12, a core component of PRC2/3, from colon cancer cells. To determine which of the putative target genes are directly bound by Suz12 and to precisely map the binding of Suz12 to those promoters, we combined a high-resolution chromatin immunoprecipitation (ChIP) analysis with custom oligonucleotide promoter arrays. We next identified additional putative Suz12 target genes by using ChIP coupled to CpG-island microarrays. We showed that HKMT-Ezh2 and Eed, two other components of the PRC2/3 complexes, colocalize to the target promoters with Suz12. Importantly, recruitment of Suz12, Ezh2 and Eed to target promoters coincides with methylation of histone H3 on Lys 27.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism
  • Colonic Neoplasms / genetics
  • Colonic Neoplasms / metabolism
  • CpG Islands
  • DNA-Binding Proteins
  • Enhancer of Zeste Homolog 2 Protein
  • Gene Expression Regulation
  • Gene Silencing*
  • Histone-Lysine N-Methyltransferase / genetics
  • Histone-Lysine N-Methyltransferase / metabolism
  • Histones / genetics
  • Histones / metabolism*
  • Humans
  • Lysine / metabolism*
  • Macromolecular Substances
  • Methylation
  • Nuclear Proteins
  • Oligonucleotide Array Sequence Analysis / methods
  • Polycomb Repressive Complex 2
  • Polycomb-Group Proteins
  • Promoter Regions, Genetic
  • Proteins / genetics
  • Proteins / metabolism
  • Repressor Proteins / genetics*
  • Repressor Proteins / metabolism
  • Transcription Factors

Substances

  • Carrier Proteins
  • DNA-Binding Proteins
  • EED protein, human
  • Histones
  • Macromolecular Substances
  • Nuclear Proteins
  • Polycomb-Group Proteins
  • Proteins
  • Repressor Proteins
  • SUZ12 protein, human
  • Transcription Factors
  • EZH2 protein, human
  • Enhancer of Zeste Homolog 2 Protein
  • Histone-Lysine N-Methyltransferase
  • Polycomb Repressive Complex 2
  • Lysine