Regulation of gene expression in developing cortex by the transcription factor Pax6

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Our knowledge of how the brain controls its own development during embryogenesis is still relatively poor. What we do know is that a relatively small group of genes, encoding proteins called transcription factors, control the processes by which cells divide, move and mature in the embryo to make the brain. These transcription factors are often thought of as master regulators of development. Severe defects can result from abnormalities in the activity of any one of these genes in humans or in other animal species, indicating their fundamental importance for normal brain development. Transcription factors work by controlling the activity of other genes; but which genes, how directly are they controlled and are different genes controlled at different times in development? These questions remain largely unanswered, although we know enough to realise that the answer will be complex, with many hundreds of genes falling under the control of each individual transcription factor.Our research is aimed at deepening understanding of the actions of one such transcription factor, Pax6. There has been sustained interest in the analysis of this particular transcription factor over many years by our group and others. Its disruption is well-known to cause severe human disease. It is a high-level regulator of the development of nerve cells in many contexts and it can programme stem cells to become nerve cells, which could be useful in the future development of new therapies based on the exploitation of stem cells. This application is timely since we have recently made and validated new transgenic mice for this work.These new transgenic lines will allow us to circumvent some of the major problems encountered in previous studies aimed at discovering and investigating the genes that Pax6 regulates at different times during development. First, they will allow us to home in on just those cells that express the Pax6 gene, in which Pax6's direct actions will be found; we shall be able to ignore those cells that no longer express Pax6 and are, therefore, no longer under its direct control even though they might still be influenced indirectly by Pax6's actions at earlier times and/ or in other cells. Second, they will allow us to test the effects of removing Pax6 at different developmental ages on the activity of other genes, providing information on which genes are controlled by Pax6 at different ages. The aim of the first part of the work will be to use experimental techniques followed by computational (bioinformatic) methods to generate and analyse large amounts of data on how loss of Pax6 at different ages affects the activity of other genes. The important outcome expected from this aspect includes robust identification of genes that are regulated by Pax6 at different developmental ages and the nature of the regulation, e.g. which genes are suppressed by Pax6, which are activated, how quickly are they affected by loss of Pax6, etc. The aims of the second part of the work will be to test specific hypotheses on whether Pax6 regulates particular genes directly or not and to correlate Pax6's actions on gene activity with its effects on how developing brain cells divide, move and mature. This will be a vital step towards the challenging goal of gaining a comprehensive understanding of the molecular functions of a key transcription factor in brain development. This work is important not only because it will tell us about Pax6's mechanisms of action: more generally, progress here will inform research in related fields, for example the analysis of genetic diseases, cancer and stem cell biology.