Protein SUMOylation and transcriptional control in a dynamic 3D chromatin environment

The decoding of our genome through the process of gene transcription ultimately dictates the form and activity of the cells in our body. Importantly, this decoding activity is not static but is dynamic and changes in response to intra and extracellular cues. These dynamic responses are controlled by pathways such as the ERK signalling cascade which ultimately impact on gene expression profiles. This pathway is important for normal cellular responses in our immune systems and brains, which enables us to function normally in combatting microbial infections and process information. Once deregulated, this pathway can lead to disease states, as exemplified by its frequent hyperactivation in cancer. Our preliminary work has shown that the target genes for this pathway exist in complex 3-dimensional environments, whereby multiple control elements cluster together. Furthermore, we demonstrate that these control elements are marked by a protein called SUMO and that this modification is dynamically deposited across genes as transcription proceeds. This is suggestive of an important role for SUMO. In this project we will examine the role of SUMO in inducible gene regulation. First we will assess the role of SUMO in creating a local 3D structure that facilitates gene expression. Next we will ask how SUMO effects gene activation and determine relevant target proteins that are involved in this process. This will enable us to understand how the switches that control gene transcription are regulated. This is important, not only in the context of ERK pathway signalling but more broadly as SUMO has been shown to play a critical role in cell fate decisions, which is of particular relevance in iPS cell generation which are the building blocks used in regenerative medicine.

Growth factor inducible gene regulation is one of the central mechanisms governing cell fate decisions. As such, this process is re-purposed in multiple contexts ranging from developmental decisions, through to immunological responses and neuronal responses in the brain. One prominent pathway is the Epidermal Growth Factor (EGF) pathway which signals from the receptor tyrosine kinase, EGFR, through intermediary proteins such as RAS and culminates in activation of the ERK protein kinase. ERK subsequently impacts on gene expression, triggering the rapid transcriptional upregulation of a cohort of genes. The importance of this pathway is further emphasised by its misregulation in a broad range of cancers, therefore understanding how growth factor signalling impacts on gene expression is a biomedically relevant endeavour. Our preliminary data demonstrate that the SUMO modification pathway plays an important role in the control of growth factor-mediated transcriptional activation. Furthermore, we have identified a complex 3D genomic environment around this class of genes, in which multiple putative enhancer elements come into close proximity with their promoters. Intriguingly these enhancers are marked with SUMO. This SUMOylation mark is unchanged after EGF stimulation but dynamic SUMOylation is observed surrounding and within the gene bodies. Collectively, these data define two potential areas for SUMO involvement in the EGF response; the first in shaping the activity of enhancers and the second in dynamically acting in the gene proximal regions. However the role of SUMO is unclear and here we will investigate its role in these two contexts. Dynamic gene regulation is a recurring theme governing cell fate decisions and understanding how 3D regulatory architectures are established and maintained is a fundamentally important facet of gene regulation. The concepts uncovered by this work therefore have the potential to impact more broadly across multiple biological systems.

Academic beneficiaries: As described in the 'Academic beneficiaries' section, these will include UK and international researchers in the following biological science fields: Gene regulation, chromatin regulation and cell signalling. 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 alternative strategies to combat cancers driven by the deregulation of growth factor pathway signalling. The lab has a track record in providing training to 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 might 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.