Promoting the loss of cell identify by erasing DNA modifications laid down throughout the genome is a critical part of cellular reprogramming – a process which has to be undergone in situations such as conception where the sperm and egg cells fuse to create the first cell of a new life. The same reprogramming process occurs in the lab when a special type of stem cell is created. These cells, called induced pluripotent stem cells (iPSCs), can become any type of cell in the body and are of particular interest for tissue engineering and regenerative medicine purposes.
Researchers at the Institute have looked more closely at what happens during the erasure of these DNA modifications, a process called DNA demethylation, to learn more about how the a cell of a determined identity can be reprogrammed back to a pluripotent stem cell. Their results are published in the journal Cell Reports today.
The researchers looked in detail across the genome to analyse the dynamics of DNA demethylation during the generation of iPSCs. They found that two different types of demethylation, widespread genome-wide (glabal) demethylation and demethylation targeted to specific parts of the genome both occur in parallel in iPSCs but that they occur by different processes.
Professor Wolf Reik, Head of the Epigenetics programme at the Babraham Institute, explains: “Reprogramming activates genes required for the pluripotent state while the genes conferring a particular cell identify are silenced. We found that two modes of DNA demethylation occur during iPSC reprogramming. There is global demethylation, which is likely to be important for erasing the cell’s memory of its original identity. And, in parallel, a targeted loss of DNA methylation at specific parts of the genome occurs which is likely to be required to establish the cell’s new pluripotent identity.”
Understanding the two distinct demethylation processes may be important in future efforts to improve the safety and efficiency of obtaining robust, high quality iPSCs for therapeutic applications in regenerative medicine.
Surprisingly, the researchers found a difference in the extent of global loss of DNA methylation marks when comparing cells taken from female or male mice. Global demethylation was more pronounced in female cells.
Dr Inȇs Milagre, previously a FEBS Research Fellow at the Babraham Institute, now Marie Curie Fellow at the IGC, Portugal, and first author in the paper commented: “Gender differences in DNA methylation patterns are known to occur in specific biological processes. However, since there are no substantial differences in global DNA methylation levels when comparing female to male fully reprogrammed iPSCs, we were surprised to see that cells from female and male mice showed such markedly different global DNA demethylation dynamics during the reprogramming process. We think that it’s likely that this is due to reactivation of the X chromosome in female cells during iPSC reprogramming. It will be interesting to investigate this further to see whether the gender specific differences in DNA demethylation seen in our experiments are connected to differences in developmental potential between female and male iPSCs”.
This research was funded by The Wellcome Trust, BBSRC, the EU Network of Excellence EpiGeneSys and a FEBS fellowship to Dr Inȇs Milagre.
Milagre et al. (2017) Gender Differences in Global but not Targeted Demethylation in iPSC Reprogramming. Cell Reports DOI: 10.1016/j.celrep.2017.01.008
Inȇs Milagre, Post-doctoral researcher (former Reik lab member)
Thomas Stubbs, PhD student (Reik lab)
Michelle King, Research assistant (former Reik lab member)
Julia Spindel, PhD student (Reik lab)
Fátima Santos, senior research scientist (Reik lab)
Felix Krueger, bioinformatician (Bioinformatics group)
Anne Segonds-Pichon, biological statistician (Bioinformatics group)Simon Andrews, Head of Bioinformatics
Wendy Dean, senior research scientist (Reik lab)Wolf Reik, Head of Epigenetics programme and group leader at the Babraham Institute, and associate faculty at the Wellcome Trust Sanger Institute
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31 January 2017