title: In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine.
abstract: Genome-wide methylation of cytosine can be modulated in the presence of TET and thymine DNA glycosylase (TDG) enzymes. TET is able to oxidise 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TDG can excise the oxidative products 5fC and 5caC, initiating base excision repair. These modified bases are stable and detectable in the genome, suggesting that they could have epigenetic functions in their own right. However, functional investigation of the genome-wide distribution of 5fC has been restricted to cell culture-based systems, while its in vivo profile remains unknown.
  
  
  
  Here, we describe the first analysis of the in vivo genome-wide profile of 5fC across a range of tissues from both wild-type and Tdg-deficient E11.5 mouse embryos. Changes in the formylation profile of cytosine upon depletion of TDG suggest TET/TDG-mediated active demethylation occurs preferentially at intron-exon boundaries and reveals a major role for TDG in shaping 5fC distribution at CpG islands. Moreover, we find that active enhancer regions specifically exhibit high levels of 5fC, resulting in characteristic tissue-diagnostic patterns, which suggest a role in embryonic development.
  
  
  
  The tissue-specific distribution of 5fC can be regulated by the collective contribution of TET-mediated oxidation and excision by TDG. The in vivo profile of 5fC during embryonic development resembles that of embryonic stem cells, sharing key features including enrichment of 5fC in enhancer and intragenic regions. Additionally, by investigating mouse embryo 5fC profiles in a tissue-specific manner, we identify targeted enrichment at active enhancers involved in tissue development.
authors.affiliation: The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK.
authors.forename: Mario
authors.identifier: 0000-0003-3919-9689
authors.initials: M
authors.lastname: Iurlaro
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
authors.forename: Gordon R
authors.initials: GR
authors.lastname: McInroy
authors.affiliation: The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK.
authors.forename: Heather E
authors.initials: HE
authors.lastname: Burgess
authors.affiliation: The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK.
authors.forename: Wendy
authors.initials: W
authors.lastname: Dean
authors.affiliation: Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
authors.forename: Eun-Ang
authors.initials: EA
authors.lastname: Raiber
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.|Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.|Present Address: Discovery Sciences, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Bachman
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
authors.forename: Dario
authors.initials: D
authors.lastname: Beraldi
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. sb10031@cam.ac.uk.|Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK. sb10031@cam.ac.uk.|School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK. sb10031@cam.ac.uk.
authors.forename: Shankar
authors.initials: S
authors.lastname: Balasubramanian
authors.affiliation: The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK. wolf.reik@babraham.ac.uk.|Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK. wolf.reik@babraham.ac.uk.|Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. wolf.reik@babraham.ac.uk.
authors.forename: Wolf
authors.initials: W
authors.lastname: Reik
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D003596:Cytosine / Q000031:analogs & derivatives*; D047108:Embryonic Development / Q000235:genetics; D004742:Enhancer Elements, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D018507:Gene Expression Regulation, Developmental; D063990:Gene Ontology; D055106:Genome-Wide Association Study; D051379:Mice; D018345:Mice, Knockout; D009928:Organ Specificity / Q000235:genetics
chemical_list: C560973:5-formylcytosine; D003596:Cytosine