Analysing the dynamics of gene regulation
We all have a complete set of DNA in each of our cells. However, far from all of the properties that DNA determines are expressed in each cell type. Gene activity in our DNA depends on all kinds of circumstances, including cell type, time, illness and the presence of hormones. This gene expression is regulated by transcription factors that temporarily bind to DNA at various sites. These regulatory proteins – there are approximately 2,600 different ones – influence the activity of genes in the DNA in their vicinity. Thanks in part to the ERC Advanced Grant just awarded to him, Frank Holstege, a Professor of Genomics, will be able to spend the years ahead analysing the dynamics of gene regulation and establishing how dynamic binding works. Holstege and his research team will do this in depth: for a whole set of transcription factors, for the full genome and for both association and dissociation.
Author: Youetta Visser
Hundreds of transcription factors
Frank Holstege grabs a piece of paper and pen and draws a sketch of the structure. He draws a straight line. "Imagine that this line is the DNA. A transcription factor moves towards this DNA, binds to it for a shorter or longer period of time and then dissociates. A lively dynamism created by hundreds of transcription factors across the entire length of the line. We already know that if a transcription factor binds to DNA, this will influence subsequent gene expression. However, the research done to date has been a mere snapshot, focusing on one regulatory protein and one gene. We want to research the dynamics involved. What activates transcription factors and what determines how long they bind to DNA and where? Our research will cover the entire genome, at every DNA binding site, consistently considering the impact that each has on the activity of genes."
Hard quantitative data
This large-scale research project will involve two methods, both of which the researchers have been developing themselves in part. One measures binding dynamics and the other dissociation dynamics. "We will start by creating the strains to test just one transcription factor: CBF1. This binds to several hundred sites, including sites at which no gene expression occurs. What makes this transcription factor so special is the different effect it has at different sites in our DNA; sometimes it represses genes and sometimes it activates them. We don't know why this is yet." The real work will start after this pilot. "The time for theorising is over. What I want to do now is to gather a large amount of hard quantitative data, obtained by asking the same questions about each transcription factor. We will then use these data to identify patterns. These, in turn, will enable us to formulate rules on the dynamics identified. Naturally, these rules will be verified too."
The dividing line between fundamental research and social relevance is blurred here. "This research is driven purely by curiosity", says Holstege, "but its impact could be huge. Differences in gene expression are responsible for a wide range of different illnesses. Added to this, the genetic predisposition that individuals have to many illnesses will depend on the sites at which transcription factors bind to DNA." If his research team is able to gain an understanding of the dynamics involved in gene regulation, the next step could be to identify how to influence these dynamics.
Seeking to identify patterns
Holstege has put together a multidisciplinary research team for his ERC research. "For example, besides molecular biologists and biochemists, half of my team consists of bioinformaticians. They determine which algorithms will be used when seeking to identify patterns in the large amount of data obtained." The research team has reserved a large amount of capacity on HPC computers, which they will use to perform the calculations. Most measurements will pertain to the DNA of yeast. "Yeast has a limited DNA – 12 million base pairs (12 Mb) – and much is already known about it. It is easy to manipulate too", the professor explains. "Although human DNA is far more complex (3000 Mb), I expect the basic principles to be largely the same. The first step will be to gain an understanding of the system and how it works."
How life works
Holstege is driven: "Genomics, the knowledge of our DNA and the corresponding research techniques, has developed rapidly in the last seven years. It is fantastic to be able to make my own contribution to these developments. My ultimate aim is to gain a better understanding of how life works and to apply this to disease."