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The answer may all come down to how a family of proteins, called Polycomb, affect cell identity and function, according to Guillermo Orsi, a staff scientist at the world-renowned INSERM in France. He should know because he has dedicated significant time and effort as a Marie Skłodowska-Curie research fellow to solving this puzzle as part of EU-funded REPLACOMB project.
Human cells are complex, from the moment they are created to their behaviour while developing and changing over time, in both normal conditions and when faced with disease. But as Orsi explains, there are clues to follow.
“While most cells in an organism contain identical genomes, each particular cell type is distinguished by a subset of genes which work together in a coordinated way, sometimes activated, sometimes repressed according to instructions from DNA,” he explains.
The Polycomb family of proteins are special in that they repress, or switch off, a different set of genes in every cell type. This is an essential part of cell identity throughout the course of cell development, and any dysfunction of this system can lead to diseases such as cancer.
“How Polycomb proteins target specific gene sets in each cell type is vital knowledge, but still not fully understood, which is why we focused on this type of repression in REPLACOMB,” says Orsi.
Polycomb paradox
A major paradox of this system is that all Polycomb proteins are present in every cell, so how they select genes that need repression in one cell, but let the same gene remain active in another is the magic key.
“Our work tried to tackle this paradox by evaluating how Polycomb proteins associate or interact with DNA in both cases, inactive and active,” he says.
To resolve this question, REPLACOMB developed a high-resolution way of observing how proteins associate with DNA along the entire genome in the Drosophila fly, a common model organism for genomic testing. This was based on the use of enzymes that destroy DNA except when it is protected by a protein that physically contacts DNA. It means that a single protein will protect less DNA than a set of proteins associating simultaneously with the same DNA molecule.
“All we had to do was use this property to cut and then analyse the size of the protected DNA, to evaluate whether proteins are alone or cooperating throughout the genome.” This exercise proved to be enlightening and surprising at the same time.
Recruiting proteins
When the REPLACOMB team first applied the high-resolution method to identify Polycomb binding to DNA, they were half expecting that it would associate, as the literature indicated, mainly with nucleosomes (scaffold proteins that organise DNA all along the chromosome).
A big surprise and something of a “eureka moment”, says the team, was to discover that Polycomb associated mainly with very defined pieces of DNA in the genome, and these particles acted as ‘recruiters’, rather than simply a home base (nucleosomes).
Previous research suggested that Polycomb proteins can associate with DNA regardless of whether the corresponding gene is repressed or not. But REPLACOMB found that there is a key difference between these configurations. The proteins in charge of the recruiting, or indeed signalling, hone in individually to DNA when there is no gene repression going on, but work in groups when they do manage to recruit Polycomb proteins onto the team, when the gene is repressed.
“Having these recruiters around doesn’t seem to be enough: they need to cooperate to get the job done,” says Orsi. This discovery opens new avenues to understand how this repressive state is maintained in particular cell types, and whether that, in turn, can be manipulated to control the changes taking place at the cell level that lead to disease, for example.
Indeed, a number of drugs targeting Polycomb function are now in clinical trials as anti-cancer treatments. Defining how Polycomb proteins assert themselves over gene activity could one day lead to totally new treatment options.
REPLACOMB’s innovative working methods are the star in the project, especially the new approach to recognising how proteins are organised along the DNA. This should prove useful in tackling other problems connected to how proteins interact with DNA, such as diseases connected to what the team calls ‘enhancer function’, including inherited blood disorders like thalassemia.
The EU support was a “priceless opportunity”, according to Orsi, giving him the chance to work and train abroad, picking up new skills and knowledge that he has been able to share with colleagues back in Europe.
The Marie Skłodowska-Curie programme was also a major boost to the scientist’s career: “Shortly after my return to my ‘home’ country France, I secured tenure as a staff researcher at the Curie Institute, one of the main players in biomedical research in France. This was only possible because of the drive to produce innovative work supported by the fellowship, which we hope will now ripple throughout the community,” he says.