Filling the Holes in our Understanding of Stem Cell Fate

How does a single-celled human embryo transform into a human body with intricate organ systems containing trillions of specialized cells? Step into any college lecture discussing this question and I bet “transcription factors” is a phrase you’ll often hear.

Transcription factors are DNA-binding proteins that act as cell fate control switches during development. For cells destined to become, say muscle tissue, transcription factors bind DNA and help activate muscle-specific genes or keep non-muscle-specific genes silent. And so it goes for all other cell types as they form inside the growing embryo.

But file this blog entry under “Hold up a moment” because in research published today in Stem Cell Reports, CIRM-funded scientists at U.C. San Diego (UCSD) pinpoint another cellular process that appears equally as important as transcription factors in cell fate decisions. The process they studied is called nonsense-mediated mRNA decay (NMD). To go into details about NMD we need to first delve a bit more into transcription factors.

A bit of molecular biology 101
When a gene is said to be activated, or “turned on”, that’s just shorthand for describing the process of transcription in which a stretch of DNA corresponding to a gene is “read” by cell machinery and transcribed into messenger RNA (mRNA). The mRNA is then translated into a string of amino acids which forms a particular protein. By binding to the DNA in the vicinity of a gene, the transcription factors provide a physical platform for the transcribing machinery to form the mRNA. Frequent transcribing leads to more mRNA and more protein.


Transcription and translation: turning genes on to produce proteins (image:


The nonsense mRNA decay (NMD) pathway (Wikipedia)

The NMD pathway regulates transcription from the opposite end of the process by promoting the degradation of mRNAs. It was once thought to only be involved in getting rid of mRNAs that contain transcribing errors but more recent studies have shown that NMD has roles in normal cell functions. For instance, the UCSD team had shown that neural stem cells contain high levels of NMD which must be reduced to allow those stem cells to specialize into neurons. In the current paper, the team sought to better understand these underlying mechanisms that enable the NMD pathway to regulate development.

To accomplish this goal, NMD function was examined during the very early stages of human development using human embryonic stem cells (hESC). All adult tissues are derived from the three germ layers that form during embryogenesis: endoderm (which gives rise to lung and gut), mesoderm (which gives rise to muscle, bone, blood) and ectoderm (which gives rise to skin and neurons). When the researchers grew the hESCs under conditions that favored endoderm formation, they observed dramatically reduced levels of NMD activity. But growing hESC toward mesoderm and ectoderm fates, led to increased levels of NMD. So these very early forks in the road of cell fate decisions led to diverging levels of NMD.

NMD activities: cell fate bystander or participant?
But does this change in NMD activity play a direct role during the specialization of hESCs? To answer this question, the team focused on the manipulating NMD activity as hESCs formed into endoderm. Instead of the natural decrease in NMD proteins during endodermal formation, NMD levels were artificially maintained at high levels. Sure enough, this hampered the ability of the hESCs to take on properties of endodermal cells and instead they kept hallmarks of stem cells. Approaching this analysis from the opposite angle, NMD factors were removed from the hESCs under conditions that should block endoderm formation. In support of the previous experiment, this artificial drop in NMD activity led to the initiation of endodermal differentiation.

Further experiments determined that NMD activity specifically inhibits TGF-b, a protein that signals cells toward an endoderm fate. Conversely, the team’s results also suggest that NMD stimulates BMP which is an important signal for a mesoderm fate. So just like transcription factors, the activity of NMD modulates the balance of other proteins which ultimately direct the fate of a cell’s identity. In fact, the TGF- b and BMP pathways themselves stimulate the actions of transcription factors so there’s likely some cooperation going with these factors and NMD. We reached out to UCSD professor Miles Wilkinson, the principal investigator for this study, to get his team’s reaction to their results:

“Most of what we know about human embryonic stem cell fate revolves around the role of factors that regulate RNA synthesis – transcription factors.  In our study, we examined the other side of the coin – the role of factors required for a selective RNA decay pathway.  We were surprised to find that not only did the NMD RNA decay pathway influence embryonic cell differentiation, but it is critical for cell fate decisions through its effect on signaling pathways.  Thus, we envisage that RNA decay pathways and transcriptional pathways converge on signaling pathways to control embryonic stem cell fate.”


And a better understanding of how embryonic stem cell fate is controlled could help optimize stem cell-based therapies for a given tissue or organ. Whatever the case, it shouldn’t be long before future college students in a developmental biology class will hear “NMD” in the same breath as “transcription factors”.


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