Mechanisms of gene regulation by CSL-Notch

The development and health of all animals, including humans, depends on them generating and maintaining the correct balance of tissues. Each tissue consists of cells with distinct characteristics and these must be made and maintained in the right proportions. Two fundamental principles underlie this: the cells must be able to communicate with each other and, in response to this between-cell communication, each must switch the activity of their genes to produce the appropriate repertoire of characteristics for their function. Our research focuses on one important pathway of cell communication, so-called Notch pathway, and we aim to discover how signals through this pathway cause specific switches in gene activities to ensure the correct cell characteristics are made. This is important not only for understanding the normal process of animal development and health, but also for diseases such as cancer that arise through inappropriate Notch signals.

Genes consist of a code, generated from the 4 different letters that make up the DNA of our genetic material, and they are further packaged in the cell to make them more or less accessible to the machinery that reads this code. There must be underlying rules that determine (1) whether or not the Notch signal is able to access a particular gene and (2) whether that access results in a productive outcome from the gene. The rules are likely to rely on information from the DNA code and from the way that the gene is packaged in each type of cell. One of our goals is to find out what these rules are. To achieve this we will take a combination of computational (code analysis) and biological (surveying the genes) approaches. For our model we use the fruitfly, as all these processes are similar across species, so we can use this simple insect to learn about the mechanisms that are relevant to humans as well. In addition, the problem we are investigating, the rules governing gene access and usage, are fundamental to biology. The tools and knowledge that we generate through our investigations are therefore likely to have widespread relevance for deciphering the genetic code.

Notch signalling, which mediates communication between cells, is essential at multiple steps in the development and maintenance of tissues. As aberrations in its regulation also contribute to many diseases, such as cancers, understanding the mechanisms at the heart of this pathway is of widespread importance for the development and health of all animals, including humans. Different cohorts of genes are regulated in response to Notch activity, depending on the cell-type. Here we propose to take an interdisciplinary approach to determine the molecular mechanisms that distinguish which genes can be accessed by the key Notch pathway DNA-binding protein, CSL, and whether that access results in productive change in gene expression when Notch is activated. In doing so we aim to address two fundamental and interrelated questions, taking an interdisciplinary and systematic approach:
1. Which aspects of the DNA sequence and chromatin landscape determine the sites that CSL occupies?
2. What co-factors are recruited with CSL, and how do they affect the transcriptional outcome of its association with DNA?
Our investigations into the mechanisms of gene regulation by CSL/Notch will not only be relevant for predicting the actions of this important pathway but will also provide a paradigm for the development of novel tools that can contribute to the understanding of transcription factor function in general.

Beneficiaries:
-Industry involved in pharmaceutical research and drug development.
-Business, industrial and public sector recruiting graduate level staff.
-The general public and schools, through our involvement in public engagement.

Benefits to industry will come from the scientific results and the methodologies we develop:
1) Notch pathway is a major target for cancer and other therapeutics. Increased knowledge about the mechanisms can lead to novel approaches for targeting the pathway and can be important in informing about unforeseen side effects. For example, our results should improve the ability to "read" better the types of targets that could be activated in a particular disease context, important because the outcomes can be very different (e.g. tumour promoting versus tumour suppressing). They could also identify novel protein:protein interactions that would be a good substrate for drug developments. Benefit is likely to be realized in the longer term 5-10 years and it would impact especially on enhancing quality of health.

2) The physicochemical modelling approaches for predicting protein-DNA interactions will provide a new tool for all sectors, including the commercial sector. Its utility could be widespread, as predictability of transcription factor target sites is one of the bottlenecks to deciphering genomic information. In addition, such protein structural approaches lend themselves to subsequent modelling and development of small compounds that interfere with those molecular interactions. For example, the prototype for a leading anti-migraine drug (Zomig) was originally discovered by our collaborator, Prof Glen, using similar computational methodologies to study membrane-bound receptors. Initial benefits (deployment of the technology) could be within 5 years, if good predictive tools for protein:DNA recognition are a successful outcome. Thus, ultimate benefits would be to economic competitiveness of UK and to enhancing quality of health.

Benefits to business, industrial and public sector recruiting graduate level staff will come from the development of relevant research sills and professional skills:
The project's interdisciplinary nature ensures that the staff will acquire a broad range of technical skills (sophisticated computational approaches, high-end genomic and molecular biology techniques, exposure to physical chemistry) which will be applicable in wide range of life sciences, pharmaceutical, computational employment. Further gains come from our international collaboration, enhancing the skills training. We note that our staff already contribute to other sectors e.g. design and implementation of computational backend at Wikipedia, enterprise programming for ING. Alongside technical skills, staff will at the same time develop generic professional skills e.g. presentational skills; writing skills; data handling, including statistics; generic computational skills; project management. Evidence of our track record in this aspect comes from subsequent employment of staff from our groups (e.g. investment banking, parliamentary advisor, publishing, venture capital advisor).

Benefits to the general public and schools, through our involvement in public engagement:
We have a strong track record in communicating modern scientific methodologies and mathematical approaches to the wider community e.g. working with Plus Magazine --a maths magazine for the lay public, part of the Millennium Mathematics Project. We further were contributing to projects at Central Saint Martins School of Art in London, where the aim has been to translate scientific principles into design models. These activities will be continued and extended to encourage scientific understanding and to extend the concepts from our research into other fields. The University of Cambridge encourages and provides excellent support for public dissemination of research through the Office of Community Affairs.