Developmental regulator genes are responsible for the activation of many ESC differentiation-pathways and, as such, they are a fundamental key to understand them. And now, research about to be published in Nature Cell Biology, reveals that these genes -always believed to be inactive in ESC before differentiation start - when apparently silent (non-active) are in fact poised, already on the first steps of gene activation only unable to go further due to the presence of repressor molecules.
These results challenge the widespread paradigm that silent genes are hidden inside “balls” of compact DNA so to escape erroneous activation, opening the door to totally new approaches for stem cells’ gene manipulation. The work also reveals how ESC development is particularly plastic with the undifferentiated cells lurking in an active/inactive state, ready to differentiate very quickly in response to the environment. Finally, the research can also have implications for the creation of stem cells from already differentiate cells since these poised genes also seem to exist in the latter group.
Embryonic stem cells are pluripotents, as they are capable of originate all the body’s cells. This is done through complex genetic programs, in which some genes are activated while others suppressed depending on the cell type and function although not much is known about the mechanisms by how this is achieved. A key element to this is to understand how “developmental regulator genes” – which are responsible for initiating ESC differentiation - are repressed before this happens while remaining ready to be rapidly activated as soon as the cell fate is determined. A clue came from recent research, which uncovered that regulator genes when silent in stem cells have, nevertheless, molecules associated with activation attached to them (in addition to repressor molecules), a characteristic that earned them the label “bivalent”.
In fact, the prevalent paradigm says that when our genes - except for a few exceptions - when not in use are hidden away inside compacted DNA protecting them from being incorrectly turned on. Only when they are to be activated will the molecule of DNA unfold, allowing access to the cellular machinery necessary for gene expression (gene expression occurs in two stages - first, DNA is copied into a RNA molecule in a process called transcription, and then this RNA is “read”, providing instructions for the production of proteins (DNA – RNA – protein).
When the observation that silent developmental regulator genes were bivalent came out, Julie K. Stock, Ana Pombo and colleagues working at Imperial College London, the CSIC, Madrid and the RIKEN Yokohama Institute in Japan wondered if these genes were really inactive or something else was occurring.
To look into this question the researchers decided to investigate the presence of RNA polymerase (RNAP) in these genes. RNAP is the enzyme – enzymes are proteins that facilitate biochemical reactions – that mediate transcription (the first step of gene expression) and, as such, its presence is a good marker for gene activation. Furthermore, RNAP can bind phosphate groups (becoming phosphorylated) in different parts of its molecule and these different RNAP forms are associated with distinct stages of transcription. For instance Ser5P (in which RNAP is phosphorylated at serine- 5) is associated with the beginning of gene activation, while Ser2P (where RNAP is phosphorylated at Serine-2) is linked to RNA elongation, a later stage than the one associated with Ser5P. This means that by looking into the amounts of different RNAP forms it is possible to understand in which part of the transcription process - if at all - the cells are found.
When Stock, Pombo and colleagues tested for different RNAP forms it was discovered that in bivalent developmental regulator genes not only there was RNAP - despite the fact that the gene was silent - but also that the DNA was open (so not in a compact mass) and being transcribed, although probably without forming full RNA molecules since there was almost no Ser2P to conclude the process.
In conclusion, developmental regulator genes in ESC when apparently silent, are, instead, “stuck” in the first steps of transcription, poised to be fully activated.
And Ana Pombo - a Portuguese scientist and the team leader – thinks this might be advantageous: “We think that the presence of RNAP at developmental regulator genes in this unusual conformation, poised to go, might allow for a better coordination of the different players during early differentiation, making the process more robust and efficient”.
The next question was how could these “poised” genes be kept safe from being wrongly activated all the time then? To answer that, Stock, Pombo and colleagues removed one repressor molecule, called Ring1, which is found attached to bivalent genes and found that they were now active. As consequence, ESC started differentiating confirming that this suppressor molecule was inhibiting transcription. However, although these genes showed now increased quantities of non-phosphorylated RNAP, both Ser2P and Ser5P levels were much the same as those found when they were silent in non-differentiating ESC, suggesting that gene activation/RNA transcription, after removal of the suppressor molecule, was occurring through an alternative and yet unknown path that did not use Ser2P.
Stock, Pombo and colleagues’ research has several implications for the understanding of ESC, starting by this unusual mechanism of RNA transcription (that does not seem to use Ser2P) present at ESC developmental regulator genes, which, if found to be unique to these genes, could be related to ESC exceptional characteristics.
Furthermore, recent research in human cells has just discovered that bivalent genes (those with activation and repression markers) are much more common that previously thought, comprising as much as 75% of all silent genes, both in stem and mature specialized cells. If Stock, Pombo and colleagues’ “poised” RNAP is also present in them this contradicts the paradigm of silent genes being kept inside compacted DNA and opens a new, exciting door in the study of gene expression/activation.
In fact, when, in different tissues and organs, some genes are turned on while others remain silent in order to create mature specialised cells, it is believed that in most cases this gene silencing is irreversible. Instead, the widespread existence of bivalent genes together with Pombo and colleagues’ results seem to indicate that silent genes are much more plastic/ flexible than previously thought as they are kept in an active/inactive state that allows a better response to environmental or developmental triggers. Even more exciting is the fact that this “non-committed” condition might mean that silent genes can revert to an active state more easily than previous thought, what can be crucial if we want to create pluripotent stem cells from mature differentiated cells.
Stock, Pombo and colleagues’ results are a small step in our knowledge of ESC but one full of possibilities, undoubtedly putting us closer to one day being able to develop stem cells therapies to replace damaged or diseased tissues and organs, or even grow stem cells outside of the body to order, that ultimate Holly Grail of stem cells clinical applications.
Piece researched and written by Catarina Amorim ( catarina.amorim at linacre.ox.ac.uk)
Catarina Amorim | alfa
Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory
How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.
Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.
The results will be published on March 22 in the journal „Astronomy & Astrophysics“.
Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...
Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.
Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...
In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...
Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.
Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...
20.03.2017 | Event News
14.03.2017 | Event News
07.03.2017 | Event News
24.03.2017 | Materials Sciences
24.03.2017 | Physics and Astronomy
24.03.2017 | Physics and Astronomy