title: A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation.
abstract: BACKGROUND
  DNA methylation (5mC) plays important roles in epigenetic regulation of genome function. Recently, TET hydroxylases have been found to oxidise 5mC to hydroxymethylcytosine (5hmC), formylcytosine (5fC) and carboxylcytosine (5caC) in DNA. These derivatives have a role in demethylation of DNA but in addition may have epigenetic signaling functions in their own right. A recent study identified proteins which showed preferential binding to 5-methylcytosine (5mC) and its oxidised forms, where readers for 5mC and 5hmC showed little overlap, and proteins bound to further oxidation forms were enriched for repair proteins and transcription regulators. We extend this study by using promoter sequences as baits and compare protein binding patterns to unmodified or modified cytosine using DNA from mouse embryonic stem cell extracts.
  
  
  RESULTS
  We compared protein enrichments from two DNA probes with different CpG composition and show that, whereas some of the enriched proteins show specificity to cytosine modifications, others are selective for both modification and target sequences. Only a few proteins were identified with a preference for 5hmC (such as RPL26, PRP8 and the DNA mismatch repair protein MHS6), but proteins with a strong preference for 5fC were more numerous, including transcriptional regulators (FOXK1, FOXK2, FOXP1, FOXP4 and FOXI3), DNA repair factors (TDG and MPG) and chromatin regulators (EHMT1, L3MBTL2 and all components of the NuRD complex).
  
  
  CONCLUSIONS
  Our screen has identified novel proteins that bind to 5fC in genomic sequences with different CpG composition and suggests they regulate transcription and chromatin, hence opening up functional investigations of 5fC readers.
authors.forename: Mario
authors.initials: M
authors.lastname: Iurlaro
authors.forename: Gabriella
authors.initials: G
authors.lastname: Ficz
authors.forename: David
authors.initials: D
authors.lastname: Oxley
authors.forename: Eun-Ang
authors.initials: EA
authors.lastname: Raiber
authors.forename: Martin
authors.initials: M
authors.lastname: Bachman
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Booth
authors.forename: Simon
authors.initials: S
authors.lastname: Andrews
authors.forename: Shankar
authors.initials: S
authors.lastname: Balasubramanian
authors.forename: Wolf
authors.initials: W
authors.lastname: Reik
mesh_terms: D000818:Animals; D002352:Carrier Proteins / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism*; D016000:Cluster Analysis; D003596:Cytosine / Q000031:analogs & derivatives / Q000378:metabolism*; D019175:DNA Methylation; D053595:Embryonic Stem Cells; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D051379:Mice; D010084:Oxidation-Reduction; D025941:Protein Interaction Mapping; D015203:Reproducibility of Results; D014158:Transcription, Genetic
chemical_list: D002352:Carrier Proteins; D002843:Chromatin; D003596:Cytosine