Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry

Nat Commun. 2015 May 20:6:7155. doi: 10.1038/ncomms8155.


The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Catalytic Domain
  • Chromatin Immunoprecipitation / methods*
  • Embryonic Stem Cells / cytology
  • Enhancer Elements, Genetic
  • Genome
  • Histone Code
  • Histones / chemistry*
  • Kruppel-Like Transcription Factors / chemistry
  • Mass Spectrometry / methods
  • Mice
  • N-Myc Proto-Oncogene Protein
  • Nuclear Proteins / chemistry
  • Octamer Transcription Factor-3 / metabolism
  • Pluripotent Stem Cells / cytology
  • Promoter Regions, Genetic
  • Protein Binding
  • Proto-Oncogene Proteins / chemistry
  • Receptors, Estrogen / chemistry
  • Regulatory Sequences, Nucleic Acid
  • Reproducibility of Results
  • Transcription Factors


  • Dppa2 protein, mouse
  • Esrrb protein, mouse
  • Histones
  • Klf5 protein, mouse
  • Kruppel-Like Transcription Factors
  • MYCN protein, mouse
  • N-Myc Proto-Oncogene Protein
  • Nuclear Proteins
  • Octamer Transcription Factor-3
  • Pou5f1 protein, mouse
  • Proto-Oncogene Proteins
  • Receptors, Estrogen
  • Transcription Factors