title: Transient accumulation of 5-carboxylcytosine indicates involvement of active demethylation in lineage specification of neural stem cells.
abstract: 5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene activity during differentiation. Tet dioxygenases oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Both 5fC and 5caC can be excised from DNA by thymine-DNA glycosylase (TDG) followed by regeneration of unmodified cytosine via the base excision repair pathway. Despite evidence that this mechanism is operative in embryonic stem cells, the role of TDG-dependent demethylation in differentiation and development is currently unclear. Here, we demonstrate that widespread oxidation of 5hmC to 5caC occurs in postimplantation mouse embryos. We show that 5fC and 5caC are transiently accumulated during lineage specification of neural stem cells (NSCs) in culture and in vivo. Moreover, 5caC is enriched at the cell-type-specific promoters during differentiation of NSCs, and TDG knockdown leads to increased 5fC/5caC levels in differentiating NSCs. Our data suggest that active demethylation contributes to epigenetic reprogramming determining lineage specification in embryonic brain.
authors.affiliation: Medical Molecular Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
authors.forename: Lee M
authors.initials: LM
authors.lastname: Wheldon
authors.affiliation: Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Abdulkadir
authors.initials: A
authors.lastname: Abakir
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Ferjentsik
authors.affiliation: School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Dudnakova
authors.affiliation: Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Strohbuecker
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Denise
authors.initials: D
authors.lastname: Christie
authors.affiliation: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors.forename: Nan
authors.initials: N
authors.lastname: Dai
authors.affiliation: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors.forename: Shengxi
authors.initials: S
authors.lastname: Guan
authors.affiliation: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Foster
authors.affiliation: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors.forename: Ivan R
authors.initials: IR
authors.lastname: Corrêa
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Matthew
authors.initials: M
authors.lastname: Loose
authors.affiliation: Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: James E
authors.initials: JE
authors.lastname: Dixon
authors.affiliation: Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: virginie.sottile@nottingham.ac.uk.
authors.forename: Virginie
authors.initials: V
authors.lastname: Sottile
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Johnson
authors.affiliation: Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: alexey.ruzov@nottingham.ac.uk.
authors.forename: Alexey
authors.initials: A
authors.lastname: Ruzov
mesh_terms: D000818:Animals; D019070:Cell Lineage; D002478:Cells, Cultured; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D058953:Neural Stem Cells / Q000166:cytology / Q000378:metabolism*; D055495:Neurogenesis; D044502:Thymine DNA Glycosylase / Q000378:metabolism
chemical_list: C560974:5-carboxylcytosine; D003596:Cytosine; D044502:Thymine DNA Glycosylase