Bookmarking stem cells

How pluripotency is maintained in dormant embryos

During embryonic dormancy many mammalian species can pause embryonic development to adjust the timing of birth with favorable environmental conditions. How pluripotent embryonic stem cells maintain their potential to differentiate into the cell types of the adult organism during this process is poorly understood. In a collaborative effort involving several groups at the MPIMG, scientists led by the lab of Aydan Bulut-Karslioglu have now identified a mechanism that protects gene regulatory elements involved in maintaining pluripotency from being silenced during dormancy. Their findings have been published in Nature Structural & Molecular Biology.

In 1957, the British developmental biologist Conrad Waddington used a series of striking metaphors to explain his concepts of development. He likened it to a landscape of valleys and hills, with a series of marbles (cells) rolling down a mountain. As they take different valleys (developmental paths), they eventually end up at the bottom (or the fully differentiated cell types). Today we know that these marbles can be rolled back up the hill, as in the case of induced pluripotent stem cells, and in some cases can even change valleys and be reprogrammed into other cell types. But what if the marbles stop in the middle of their tracks? This is what happens during embryonic dormancy. This adaptive strategy is characterized by a temporary halt in development, during which pluripotent stem cells retain their developmental potential. To understand how this happens, the scientists have now turned to the epigenetic landscape of dormant embryos using embryonic stem cells as a model system.

Protection from epigenetic silencing

As it turns out, while the marble is developmentally halted in its track, its epigenetic profile progresses towards differentiation. First, they profiled the DNA methylation state of dormant embryonic stem cells and embryos. Methylation is an epigenetic modification that affects gene expression without altering the DNA sequence itself. It is generally associated with reduced gene expression and silencing, providing an obvious entry point to into the epigenetic mechanisms of dormancy. "Indeed, we observed an increased methylation of dormant cells compared to their proliferating counterparts," explains Maximilian Stötzel, a PhD student and first author of the study. "However, certain sites with regulatory elements are protected from this general increase in methylation by so-called TET (ten-eleven translocation) enzymes". These enzymes are important for removing methylation marks. Group leader Aydan Bulut-Karslioglu adds: "The regulatory elements turned out to be specific regulators of pluripotency. Protecting these elements is necessary to maintain the further developmental potential of the embryo. In TET knockout models, we observed that dormant cells and embryos lose their pluripotency features."

A genetic bookmark

Digging deeper, the scientists made other surprising discoveries. "We saw that these sites are targeted not only by TET enzymes, but also by transcription factors," says Maximilian Stötzel. Transcription factors are proteins that bind to DNA sequences and activate or repress them. The scientists found other epigenetic markers that would indicate to a permissive environment, or in other words, increased gene activity. Unexpectedly, however, the binding of transcription factors did not cause transcription. "We think that the combined activity of TET enzymes and transcription factors places a kind of bookmark on the regulators of pluripotency in the dormant state, which primes cells to quickly return to the original pluripotent state," he adds. This bookmarking mechanism is a fascinating discovery, as Aydan Bulut-Karslioglu points out: "It goes against the common understanding of how genes are regulated. Normally, the combined effect of gene regulatory elements bound by transcription factors with high levels of histone acetylation creates an environment in which transcription can take place. Here, it does not lead to transcription, but rather serves as a mechanism to safeguard the pluripotent state for quick reactivation." With this insight into to the epigenetic regulation of embryonic dormancy, many questions remain about the mechanism and the players involved. "My goal is now is to identify other transcription factors and epigenetic mechanisms to understand how they crosstalk and integrate them into an even bigger picture of dormancy," concludes Aydan Bulut-Karslioglu.