Acetylation cofactors in closed chromatin - a novel mechanism of pioneer factor action and dynamics

All the cells in the human body contain the same DNA and the same set of genes. The various cells are different and have distinct functions because specific genes are turned on or off in different cell types. Regulation of gene expression is a highly complex process that is controlled by a group of proteins named transcription factors. In order to regulate expression of genes some transcription factors, named pioneer factors, binds to DNA as well as the proteins that DNA is wrapped around in the cell nucleus, named histones. The complex of DNA and histones is known as chromatin and can be found in an open state associated with active gene expression, as well as a closed and more compact state where genes are turned off. Pioneer factors are the first transcription factors to access a silent gene and initiate its expression by increasing the accessibility of DNA. This represents an essential step in the control of cell fate during early development and pioneer factors have a critical role in cell development and identity. Furthermore, pioneer factors are key drivers of the changes in transcriptional programs seen in the development of cancer. The emerging role of pioneer factors in cancer development makes them attractive therapeutic targets, but their mechanism of action is poorly understood and crucial to understand in order to therapeutically target them. The primary objective of this project is to identify this mechanism by using the cancer-associated proteins Sox9 and c-Myb as model pioneer factors. We have found that Sox9 is able to program cells towards a mesenchymal fate by acting as a pioneer factor, while c-Myb pioneer factor activity inhibits hematopoietic differentiation. We intend to identify a shared mechanism of these two pioneer factors that can also be applicable to other pioneer factors operating in other cell types. By identifying the mechanism of action of pioneer factors, this project will provide important knowledge that is relevant to the cancer field and can become the foundation of future efforts to reliably target pioneer factors therapeutically. The project is a collaboration between the Department of Biosciences, University of Oslo, and Terry Fox Laboratory, one of the research institutes of the BC Cancer Agency, in Vancouver, Canada.

We aimed to identify molecular mechanisms of pioneer factors. We have revealed details on SOX9 pioneer factor activity upon endothelial-to-mesenchymal (EndMT) transition and c-Myb pioneer factor functions in hematopoietic cells, as well as looked into c-Myb's potential role in endothelial-to-hematopoietic transition. EndMT is crucial for embryonic development, but it also plays an important role in the pathogenesis of several human disorders, including cancer progression and vascular diseases. Our study highlights the crucial developmental role of SOX9 and provides new insight into key molecular functions of SOX9 and mechanisms of endothelial-to-mesenchymal transition. Inappropriate overexpression and genomic rearrangements of the gene encoding c-Myb is associated with human leukemogenesis, highlighting the importance of resolving its mechanisms in hematopoietic cells. We anticipate that our findings will contribute to future efforts to reliably target pioneer factors therapeutically.

Pioneer factors are a subclass of transcription factors that are able to associate with closed chromatin and cause chromatin opening, allowing other DNA-binding proteins to bind and activate cell-type specific transcriptional programs. They are commonly found bound to enhancers before activation of gene expression and are crucial for the activation of genes involved in lineage determination and cell development. The emerging role of pioneer factors in cancer development makes them attractive therapeutic targets, but their mechanism of action is poorly understood and crucial to understand in order to therapeutically target them. The primary objective of this proposal is to identify this mechanism. Based on observations in the lab and from the literature, we propose a very specific mechanism of pioneer factors whereby they recruit histone acetyltransferases to closed chromatin and function as acetylation cofactors by presenting histone tails for acetylation, which in turn opens chromatin and activates enhancers. Furthermore, we propose that histone acetylation strongly impairs the binding of pioneer factors to chromatin and affects their binding dynamics, which is a novel outcome of histone acetylation and important to understand the histone code at enhancers. As a second objective, we wish to further our knowledge of the involvement of pioneer factors in human disease by identifying the genes dependent on pioneer factor action in specific cell types, as well as the cellular outcomes. We will use the cancer-associated proteins Sox9 and Myb as model pioneer factors in chondrogenesis and haematopoiesis respectively, to identify a shared mechanism that can also be applicable to other pioneer factors operating in other cell types. By identifying the mechanism of action of pioneer factors, this project will provide important knowledge that is relevant to the cancer field and can become the foundation of future efforts to reliably target pioneer factors therapeutically.