4DCellFate

Developing a global understanding of the PRC and NuRD complexes in stem cell differentiation and in disease

Project background

The goal of 4DCellFate is to elucidate how two regulatory complexes, Polycomb repressive complex 1 (PRC1) and nucleosome remodeling and deacetylation (NuRD), regulate epigenetic modifications during two different types of cellular transitions: between embryonic stem cells (ESCs) and their differentiated end stages, and between normal cells and cancer cells.

What are epigenetic modifications?

Simplistically, these are changes made to chromatin (DNA packed into structures by histones) and can occur both on the DNA directly (e.g. DNA methylation) and at the histones, on their “tails” that extend out of the nucleosome packaging structures (e.g. methylation of a lysine). Such changes can then affect the ability of the genes encoded in the DNA to be expressed or not, for example by opening up the chromatin structure or by helping to recruit factors necessary for transcription. Importantly, epigenetic changes are dynamic and can determine the fate of the cell in which they occur, allowing two cells with identical genetic content (such as stem cells) to respond to cues in different ways. Interestingly, and seemingly contradictory, epigenetic changes can be dynamic, but they can also be stably inherited (also through germ lines and thus from parents to children). (see also the overview on Scitable).

The fate of each cell is determined individually.

This is best exemplified by stem cells*, which have the potential to renew indefinitely; once they “decide” to differentiate, each stem cell can potentially differentiate into one of any of the different types of cells in the body. This implies that, once such a cell fate decision is made, a massive wave of changes must be immediately made in determining which genes are on and which are off: those that maintain the renewal potential must be switched off, those that are necessary to begin the cell differentiation program must be turned on, and those that are required for alternative cell types that were not chosen must be silenced forever. Studying how such cell fate decisions are taken mechanistically is an extremely important question, especially considering that consequences of misregulation of such programs can have severe consequences, such as cancer formation. These two types of transitions, from stem cells to differentiated cells and from normal cells to cancer cells, will be examined in the 4DCellFate project.

Why focus specifically on these two epigenetic regulatory complexes? 

The Polycomb repressive complex 1 (PRC1) and the nucleosome remodeling and deacetylation (NuRD) complex are large, multi-protein complexes with “core” of 400 to 700 kDa. Both complexes interact with numerous different regulatory partners, as well as with nucleosomes and nucleic acids, and have been shown to propagate the epigenetic memory of cells. Importantly for the 4DCellFate project, both complexes are involved in regulating stem cell differentiation and have been implicated in cancer. Both complexes are conserved from Drosophila to humans, yet in humans (and higher eukaryotes), their the regulatory function can be fine-tuned by incorporating variants of the different components.

Why should 4DCellFate succeed in addressing such an ambitious project?

4DCellFate has numerous factors that arguing for a successful outcome: i) The consortium comprises scientists who are among the best in their fields, from both academia and industry. The project will promote active collaboration between them and their laboratories, supported by numerous opportunities to network. ii) The timing is right. Massive technological leaps have been made in recent years that allow us to address heretofore impossible questions, and the expertise of the scientists within the consortium in these cutting-edge technologies will allow them to be implemented in the project. Such technologies include: “ChIP-seq” (chromatin immunoprecipitation with massively parallel DNA sequencing), which allows a map of transcription factor binding to be made over the entire genome at a given time point, and “RNA-seq” (high-throughput sequencing of cDNA, to obtain information about the RNA content), which makes it possible to analyze the complete transcriptome of a given cell type. iii) The project researches all aspects of the complexes, from A to Z: What are the structures of the complexes (and not only the complex components)? What are their interaction partners, and do these change during the cell fate transitions? Do they have function-specific components? How much of the epigenetic regulation during cell fate decisions is guided by these complexes? What are the biological consequences of specifically depleting components of the complexes?

*Ethical use of embryonic stem cells:

Based on our proposal to use human and mouse embryonic stem cells (ESCs), the 4DCellFate project underwent extensive review to assure it complied with ethical restrictions on ESC use, at the European as well as at the national level for all countries involved. Only hESCs from 4 well-established hESC cell lines will be used; thus, no human embryo tissue will be handled. Further, we have established an independent ethical advisory board that consists of two world-renown experts in the use of human and mouse ESCs: Dr. Anna Viega and Prof. Guiseppe Testa. Our advisory board will participate to the greatest degree possible in our internal scientific meetings in which we present our preliminary results and will have complete access to our data and protocols.