Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives

Cell. 2013 Feb 28;152(5):1146-59. doi: 10.1016/j.cell.2013.02.004. Epub 2013 Feb 21.

Abstract

Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass-spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells (NPC), and adult mouse brain tissue. Readers for these modifications are only partially overlapping, and some readers, such as Rfx proteins, display strong specificity. Interactions are dynamic during differentiation, as for example evidenced by the mESC-specific binding of Klf4 to mC and the NPC-specific binding of Uhrf2 to hmC, suggesting specific biological roles for mC and hmC. Oxidized derivatives of mC recruit distinct transcription regulators as well as a large number of DNA repair proteins in mouse ES cells, implicating the DNA damage response as a major player in active DNA demethylation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / analysis*
  • 5-Methylcytosine / metabolism
  • Animals
  • Brain / cytology
  • Brain / metabolism
  • Cytosine / analogs & derivatives*
  • Cytosine / analysis
  • Cytosine / metabolism
  • DNA Glycosylases / metabolism
  • DNA Methylation*
  • DNA-Binding Proteins / metabolism
  • Embryonic Stem Cells / metabolism
  • Mass Spectrometry
  • Mice
  • Oxidation-Reduction
  • Proto-Oncogene Proteins / metabolism
  • Regulatory Factor X Transcription Factors
  • Stem Cells / metabolism
  • Transcription Factors / metabolism
  • Ubiquitin-Protein Ligases / metabolism

Substances

  • DNA-Binding Proteins
  • Proto-Oncogene Proteins
  • RFX5 protein, mouse
  • Regulatory Factor X Transcription Factors
  • TET1 protein, mouse
  • Transcription Factors
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Cytosine
  • UHRF2 protein, mouse
  • Ubiquitin-Protein Ligases
  • DNA Glycosylases