A new variant of polymerase in embryonic stem cells
Embryonic stem cells face a silencing challenge. They are characterised by their unique capacity to differentiate into any type of cell in the body. This process of commitment into a specific cell lineage involves the activation of select genes.
What could be more problematic, however, is that these genes need to remain silent in embryonic stem cells, but be ready for activation and expression at a later stage of development. How this balance is maintained is a question of great interest if we are to truly harness the potential of stem cells in medicine.
Scientists have long known that proteins in the Polycomb family play an important role in silencing genes in embryonic stem cells. It was known that these genes were already primed for activation with characteristics of open chromatin. But it was unclear whether such priming was accompanied by the presence of RNA Polymerase II, which prompts transcription of DNA into RNA (the first step in gene expression). How these players might interact remained a matter to be fully resolved. New research from the CSC’s Genome Function Group, led by Ana Pombo, helps explain the unique relationship underlying the mechanism of gene silencing and expression in embryonic stem cells.
Published in the journal Cell Stem Cell, the study reveals that the RNA polymerase involved is a unique variant (RNAPII-S5p), specifically associated with Polycomb repression. “The polymerase II identified at genes repressed by Polycomb is an unusual form, never described before. It’s not like an active polymerase,” explains Emily Brookes one of the study’s lead authors. “In the past, we imagined the interplay between Polycomb and RNA polymerase as a balance between activation and repression. That would suggest that if you have more polymerase you would have less Polycomb, and vice-versa. But what we see is the opposite. This isn’t a balancing act – they’re working together.”
Using a technique called sequential ChIP, Emily could confirm that the Polycomb repressor complex and RNA polymerase variant physically bind to the same chromatin. This “functional synergy” allows the two complexes to cooperate to regulate gene expression across the whole genome.
Contrary to expectations, not all genes identified as Polycomb targets are silenced. Analyses of genome-wide data, performed by the second lead author, Ines de Santiago, are based on averages across millions of cells, and when looking at the whole population, the team identified a cohort of genes bound by Polycomb that were being actively expressed. These genes were also bound by another, active, form of RNA polymerase II. Unlike in the silenced genes, here Polycomb and the active RNA polymerase bind separately. “It seems they are either cycling on and off, or that some cells have different marks to others,” says Brookes.
“This suggests a novel ‘switch’ mechanism of gene regulation by Polycomb, where expression is ‘on or off’ in different proportions of cells, or at different times.” The cohort of genes examined is involved in metabolism, and embryonic stem cells are known to have unique energy metabolism.
The team’s data are now publicly available, and they hope that researchers around the world will continue to mine them for valuable information. Studies such as these are important steps in the advancement of stem cell use in regenerative medicine.
-AL
Reference:
Brookes, E., de Santiago, I., Hebenstreit, D., Morris, K. J., Carroll, T., Xie, S. Q., Stock, J. K., Heidemann, M., Eick, D., Nozaki, N., Kimura, H., Ragoussis, J., Teichmann, S. A., Pombo, A., Feb. 2012. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell stem cell 10 (2), 157-170.
Link to article.
