Investigating retrotransposon-driven gene expression programmes in early development

After fertilization, a single zygote proceeds through a series of cleavage steps to develop into a multicellular embryo, called a blastocyst. The cells of the blastocyst are capable of generating all adult cell types, a phenomenon known as pluripotency. The inner cell mass (ICM) of the blastocyst can moreover be cultured in a dish as pluripotent embryonic stem cells (ESCs). ESCs have become invaluable tools in regenerative medicine and to study development itself. With 1 in 8 couples experiencing infertility in the UK, it is ever more important to understand the factors contributing to healthy embryo development.

Transposable elements (TEs) are parts of our DNA that are currently or historically mobile, -i.e. having the capacity to 'paste' themselves into new places in the genome. Many TE sequences used to be thought of as simply 'junk DNA'; however, we are beginning to understand that TEs have evolved to play new and unexpected roles in development and disease. For example, uncontrolled TE activity has been implicated in neurodegeneration and cancer. However, the expression of many TEs is also high in normal development, suggesting that they may also have beneficial roles in cells.

This proposal focuses on exploring the function and regulation of a particular TE, called mouse endogenous retrovirus type L, MERVL. MERVL is the earliest expressed TE, and is transiently upregulated in mouse embryos at the 2-cell stage. This stage, conserved in human in 4-8 cell embryos, encompasses an essential process called Zygotic Genome Activation, when the embryo begins to turn on its own genes for the first time. These embryos are also considered "totipotent", meaning that they can not only generate embryonic tissues but also extra-embryonic tissues (like placenta). Interestingly, a small proportion of ESCs transiently become "2C-like" in normal culture, also possessing enhanced developmental potency. Here, we will use mouse ESCs and mouse embryos to investigate how and why MERVL regulation is important in early development. Using these tools, we will identify and characterize key factors required to activate and repress MERVL. In turn, we will investigate how these factors regulate the 2-cell stage, and affect ZGA and totipotency. To understand how MERVL and other TEs are directly regulated, we will combine genome-editing systems, called CRISPR/Cas9, with recent biochemical tools to pull out sets of proteins that bind MERVL. Lastly, we will explore the conservation of MERVL function and regulation in human cells, where a similar TE, HERVL, is known to play a conserved role. We aim to a) understand how HERVL regulates the 4-8 cell stage and human ZGA b) investigate how new HERVL regulators might contribute to specific cases of disease. These studies will significantly increase our understanding of how TEs contribute to early development, and will shed insight on how such processes are perturbed in disease.

This work encompasses the intersection of transposable elements (TEs) and early development. TEs, also known as "jumping genes", are highly abundant in organisms from plants to humans. Therefore scientific advances are broadly applicable to many fields and model organisms. This highly novel research area bridges two seemingly unrelated topics, transposon biology and developmental biology. Details of the academic impact are given in the academic beneficiaries section.

The potential economic and societal impacts of this research are significant. The main beneficiaries of the research impact will be patients, health researchers and practitioners, and R&D industries. There will also be broader benefits for the UK as this is a novel area of research capitalizing on UK expertise in epigenetics and developmental biology. Improving the understanding of the roles of TEs in early development will help inform future research and treatments for genetic diseases and improvements in the conditions of IVF. To expedite knowledge transfer to these audiences, I will strive to publish Open Access and upload manuscript preprints to BioRxiv when possible.

10% of couples experience fertility issues in the UK, with unknown mechanisms. Since this proposal focuses on the earliest stages of embryogenesis, insights gained by my research may lead to improving IVF conditions, or may identify mutations contributing to early embryo defects and infertility. The long-term benefit would be improved UK reproductive health, reduction in fertility treatment costs due to identification of embryo defects, and improved mental health of the expectant parents.

The misregulation of the processes that will be directly studied here in mouse development are involved in several diseases. This research will uncover new MERVL regulators in Aim 2, which will be explored in the context of human disease in years 5-7. Top candidates may represent novel therapeutic targets in two human diseases where MERVL/Dux homologs (HERVL/DUX4) are misregulated. The first disorder is Facioscapulohumeral Muscular Dystrophy (FSHD), which is driven by DUX4, and affects 870,000 adults and children worldwide. Secondly, DUX4 also causes a highly aggressive cancer called a sarcoma (CIC-DUX4 sarcoma, CDS). Novel regulators of DUX4 in these contexts could be explored by pharmaceutical companies as therapeutic targets. This will benefit UK Industry/Pharma, and long-term may lead to improved health or quality of life for FSHD or CDS sufferers.

Finally, as research on TEs is highly novel, I will inform and engage the wider public throughout the fellowship about TEs and their roles in development. The general view is either that TEs are "junk DNA" in our cells, or people are unaware that they exist at all. Through progressive engagement activities through a series of platforms I will inform and engage target audiences about the "real" roles of junk DNA in our cells and impress upon the audience how much we still have yet to find out. I will listen to the audience and use this to inform future engagement activities, leading to increased public awareness in the UK about TEs, and interest in science overall. One key audience which I will target are women and girls. Public perceptions of scientists are gradually changing, but women are still strikingly underrepresented in science leadership positions. As a female group leader, it is important that I utilize this platform to speak out and inspire women to one day consider a career in science. I will combine discussions on my research with career advice, mentoring, and advocacy to promote women in science. This will contribute to shifting the scientific stereotype and empowering women not only to try a career in STEM, but also to aim to be a leader in the field. Given Barbara McClintock's (Nobel Prize 1983) revolutionary discovery of TEs, this is a highly relevant field to encourage the achievements of female scientists.