Establishing and maintaining regulatory competency in the human genome.

As we age, we lose the capacity to repair damaged tissues and organs. One reason for this is due to the loss of a specialised set of cells known as stem cells. These cells have the capability of restoring damaged cells and have the potential to change their identity to produce multiple different cell types. This property has led researchers to try to use these cells in regenerative medicine to make cells in the laboratory which can replace damaged cells in our body. However to undertake this process it is important to understand how stem cells can change into other cell types. Part of the answer to this, is a change in how their control systems are wired, and how their DNA is packaged up. This project will investigate how a molecular switch, known as the FOXK2-SIN3A protein complex, contributes to this rewiring process. We will conduct our studies in human embryonic stem cells and examine the molecular events that occur as these cells change fate to create different cell types. Our findings will help us understand how stem cells can change their identity, and potentially will provide us with mechanistic information that enables us to both improve this process for therapeutic benefit and to understand how age related diseases develop.

There is currently intense interest in human stem cells and their potential therapeutic value in regenerative medicine. Molecularly, it is important to understand how the chromatin, and hence gene regulatory, landscape changes as stem cells differentiate to defined cell types. The precise establishment of the correct regulatory landscape is thought to be a key element in generating cells which are going to be of long term therapeutic value with no associated unwanted side effects. Here we will study how regulatory elements are initially established in human embryonic stem cells and maintained for subsequent use in differentiated cell types. Our preliminary work indicates that the FOXK2-SIN3A transcription factor complex demarcates regulatory regions in the chromatin of embryonic stem cells. Typically, this complex is thought to be repressive in nature due to its association with histone deacetylases but we find that it is associated with active genes and areas of the genome that are destined for activation during the early stages of cellular differentiation. One potential role for the FOXK2-SIN3A complex in this context is to maintain regulatory regions in an activation competent state through balancing out histone acetylase activity. In this context, FOXK2 binding could also act directly as a licencing factor for the recruitment of other tissue-specific transcription factors. In this project we will focus on the role of the FOXK2-SIN3A complex in establishing and maintaining the regulatory chromatin architecture of embryonic stem cells. We will first determine the role of FOXK2 in establishing regulatory region competency in embryonic stem cells. We will then focus on whether an acetylation equilibrium is important in maintaining regulatory region activity. Finally, we will determine how FOXK2 binding influences the recruitment of other tissue-specific transcription factors as differentiation proceeds.

Academic beneficiaries: As described in the 'Academic beneficiaries' section, these will include UK and international researchers in the following biological science fields: Gene regulation, stem cell research, chromatin regulation and transcription factor function. Academic beneficiaries from other disciplines will include clinical researchers studying disease states involving deregulated enhancer function, including cancer. Finally, bioinformaticians and mathematical modellers studying dynamic transcriptional networks will benefit from our research as we aim to identify novel regulatory nodes. We will publicise our work by publishing in high impact scientific journals, regular presentation at International conferences, and posting on our laboratory and Faculty websites.

General public: In terms of the wider public beneficiaries, the long term impact of this project will likely be for cancer patients or patients requiring stem cell based therapeutic treatments. Our work will uncover fundamental mechanisms involved in establishing and maintaining regulatory regions of the genome, and this knowledge can be used to understand and develop strategies to combat inappropriate regulatory region activation in cancer cells and improve stem cell differentiation and dedifferentiation protocols. We aim to encourage the next generation to become engaged in scientific research through hosting school children in the laboratory. Our work will be communicated to the general public through local charity events and science festivals. Important findings will be communicated through the standard media outlets.

Public sector: As this is a basic research project, there will be no immediate impact on the public sector. However, in the long term the biggest impact is likely to be on the NHS. Any new mechanisms that we identify might lead to improved stem cell based therapies and hence will contribute to regenerative medicine. The lab has a track record in providing training medically qualified MD and PhD students and the work on this project will provide a solid framework and more openings for these students who wish to develop clinically relevant projects on the non-coding regulatory elements of the genome and their deregulation in cancer or other disease states.

Industry: There is growing interest from Biotechnology companies in developing stem cell based therapies. One of the key elements in developing new cell types from stem cells is establishing the correct gene expression profiles and this is in turn dictated by remodelling the chromatin landscape which involves regulatory element establishment, maintenance and activation. Our work may therefore dictate ways in which differentiation and de-differentiation protocols can be enhanced to provide high fidelity production of specific cell types.
This project will also involve the use of many cutting edge technologies, especially related to systems based approaches to research and advanced bioinformatics and computational skills. As such the project will provide an opportunity for training the next generation of researchers through exposing undergraduate, postgraduate and postdoctoral students in the lab to these approaches.