Title |
Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems
|
---|---|
Published in |
Genome Biology, February 2015
|
DOI | 10.1186/s13059-014-0576-y |
Pubmed ID | |
Authors |
Colm E Nestor, Raffaele Ottaviano, Diana Reinhardt, Hazel A Cruickshanks, Heidi K Mjoseng, Rhoanne C McPherson, Antonio Lentini, John P Thomson, Donncha S Dunican, Sari Pennings, Stephen M Anderton, Mikael Benson, Richard R Meehan |
Abstract |
BackgroundThe DNA methylation profile of mammalian cell lines differs from the primary tissue 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.ResultsWe demonstrate that adaptation of mouse embryonic fibroblast, MEFS, 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.ConclusionsWe 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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 6 | 25% |
United States | 5 | 21% |
Australia | 2 | 8% |
France | 2 | 8% |
New Zealand | 1 | 4% |
Unknown | 8 | 33% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 14 | 58% |
Scientists | 7 | 29% |
Science communicators (journalists, bloggers, editors) | 3 | 13% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 6 | 2% |
United Kingdom | 2 | <1% |
Switzerland | 1 | <1% |
France | 1 | <1% |
Sweden | 1 | <1% |
Singapore | 1 | <1% |
Austria | 1 | <1% |
Korea, Republic of | 1 | <1% |
Mexico | 1 | <1% |
Other | 2 | <1% |
Unknown | 253 | 94% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 71 | 26% |
Researcher | 54 | 20% |
Student > Bachelor | 32 | 12% |
Student > Master | 28 | 10% |
Student > Doctoral Student | 14 | 5% |
Other | 40 | 15% |
Unknown | 31 | 11% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 97 | 36% |
Agricultural and Biological Sciences | 84 | 31% |
Medicine and Dentistry | 17 | 6% |
Engineering | 9 | 3% |
Neuroscience | 5 | 2% |
Other | 18 | 7% |
Unknown | 40 | 15% |