title: Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems.
abstract: BACKGROUND
  The DNA methylation profiles of mammalian cell lines differ from those of the primary tissues from which they were derived, exhibiting increasing divergence from the in vivo methylation profile with extended time in culture. Few studies have directly examined the initial epigenetic and transcriptional consequences of adaptation of primary mammalian cells to culture, and the potential mechanisms through which this epigenetic dysregulation occurs is unknown.
  
  
  RESULTS
  We demonstrate that adaptation of mouse embryonic fibroblasts to cell culture results in a rapid reprogramming of epigenetic and transcriptional states. We observed global 5-hydroxymethylcytosine (5hmC) erasure within three days of culture initiation. Loss of genic 5hmC was independent of global 5-methylcytosine (5mC) levels and could be partially rescued by addition of vitamin C. Significantly, 5hmC loss was not linked to concomitant changes in transcription. Discrete promoter-specific gains of 5mC were also observed within seven days of culture initiation. Against this background of global 5hmC loss we identified a handful of developmentally important genes that maintained their 5hmC profile in culture, including the imprinted loci Gnas and H19. Similar outcomes were identified in the adaption of CD4(+) T cells to culture.
  
  
  CONCLUSIONS
  We report a dramatic and novel consequence of adaptation of mammalian cells to culture in which global loss of 5hmC occurs, suggesting rapid concomitant loss of methylcytosine dioxygenase activity. The observed epigenetic and transcriptional re-programming occurs much earlier than previously assumed, and has significant implications for the use of cell lines as faithful mimics of in vivo epigenetic and physiological processes.
authors: Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden. colm.nestor@liu.se.|MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. colm.nestor@liu.se.
authors: Colm E
authors: CE
authors: Nestor
authors: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. Raffaele.Ottaviano@igmm.ed.ac.uk.
authors: Raffaele
authors: R
authors: Ottaviano
authors: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. diana.reinhardt@uni-ulm.de.
authors: Diana
authors: D
authors: Reinhardt
authors: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. hcruicks@staffmail.ed.ac.uk.
authors: Hazel A
authors: HA
authors: Cruickshanks
authors: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. heidi.mjoseng@igmm.ed.ac.uk.
authors: Heidi K
authors: HK
authors: Mjoseng
authors: MRC Centre for Inflammation Research, Centre for Multiple Sclerosis Research and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, EH16 4TJ, UK. R.McPherson@ed.ac.uk.
authors: Rhoanne C
authors: RC
authors: McPherson
authors: Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden. antonio.lentini@liu.se.
authors: Antonio
authors: A
authors: Lentini
authors: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. John.Thomson@igmm.ed.ac.uk.
authors: John P
authors: JP
authors: Thomson
authors: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. Donncha.Dunican@igmm.ed.ac.uk.
authors: Donncha S
authors: DS
authors: Dunican
authors: Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK. Sari.Pennings@ed.ac.uk.
authors: Sari
authors: S
authors: Pennings
authors: MRC Centre for Inflammation Research, Centre for Multiple Sclerosis Research and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, EH16 4TJ, UK. Steve.Anderton@ed.ac.uk.
authors: Stephen M
authors: SM
authors: Anderton
authors: Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden. mikael.benson@liu.se.
authors: Mikael
authors: M
authors: Benson
authors: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. Richard.Meehan@igmm.ed.ac.uk.
authors: Richard R
authors: RR
authors: Meehan
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism / Q000031:analogs & derivatives; D000220:Adaptation, Biological / Q000235:genetics; D000818:Animals; D018929:Cell Culture Techniques / Q000379:methods*; D002478:Cells, Cultured; D065150:Cellular Reprogramming / Q000235:genetics*; D003596:Cytosine / Q000031:analogs & derivatives / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D049308:Dioxygenases / Q000378:metabolism; D044127:Epigenesis, Genetic; D005347:Fibroblasts / Q000378:metabolism; D056426:Genetic Loci; D008322:Mammals / Q000235:genetics*; D008810:Mice, Inbred C57BL; D059467:Transcriptome / Q000235:genetics*
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D049308:Dioxygenases
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