Microarray analysis for studies of genome organisation and evolution plus development of novel diagnostic tools and technologies

A microarray is a series of tiny spots of DNA arranged on a glass slide in a very ordered way. It can represent a whole genome, ordered as it appears in the organism; it can consist of parts of genes that are expressed in certain tissue at certain times or it can contain DNA that represents the sort genetic of variation that would appear in individual organisms such as ourselves. When we perform certain experiments on these arrays we can better understand when genes are switched on and off at certain developmental time-points, how humans and animals vary genetically and how genomes evolve. Previously my research interests have centred around the studies of chromosomes - the structures that form from the DNA (and associated protein) as a cell divides. Notable successes include the first application of a chromosomal technique for diagnosing genetic disease in embryos only three days after they have been conceived, insight in to sperm production and telling all the chromosomes apart in chicken (the first time this had been achieved in a bird). More recently we have been interested in what happens to the chromosomes when the cell is not dividing i.e. when the cell is performing its normal functions. The opportunity to introduce microarray technology into my laboratory is an exciting one. In principle, a lot of the technology is very similar to that used on chromosomes and thus should not present a quantum leap, particularly if I can attend certain training courses to get me up to speed with respect to protocols for analysing the results obtained. These courses are run regularly e.g. at the Sanger Centre in Cambridge. Specifically, I would be interested in developing new microarray-based technologies for genetic diagnosis in early development; investigating genome evolution in birds; and asking how the switching on and off of genes and gene clusters relates to their position in space and time in the nucleus of a cell. Funding is requested therefore to buy out my time from my teaching and administration duties to re-direct my own interests and that of my laboratory towards this novel technology and, more specifically, asking biological questions using it.

The purpose of this application is to seek funds to establish microarray technology in my laboratory to pump-prime a high-impact research effort with three areas of interest: 1. Development of tools and technologies for preimplantation diagnostics and to provide insight into aneuploidy origin I first reported preimplantation diagnosis by FISH in the early 1990s; since then, diagnosis is still limited to around eight chromosomes per nucleus. Microarray makes it possible to determine copy number for all chromosomes by CGH and exploit high-density SNP arrays, analysing amplified DNA from both parents and fetus to determine the parent and stage of origin and the determination of the degree and position of cross-over events. 2. Correlation of gene expression and nuclear organisation Studies of nuclear organisation concerned with the three and four-dimensional topology of the interphase nucleus, are thought to be key to understanding large-scale transcriptional regulation and mediation of normal/abnormal cellular function. Previous studies have implicated either a gene density or chromosome size determined arrangement for whole chromosomes. Further studies have addressed individual loci in relation to transcriptional activity. There is however a poorly understood meso-scale between these two extremes. The purpose of the proposed programme of research will be to combine transcription profiling with nuclear organisation studies to investigate the degree to which changes in three-dimensional nuclear organisation are responsible for the transcriptional changes in developing cells. Test systems will include mammalian spermatogenesis and avian macrophage activation. 3. Investigation of chromosome rearrangements in birds Here I will apply labelled chromosome paints directly on to the recently developed chicken tiling path microarray. Careful molecular identification of breakpoints/fusion points will shed light into the mechanisms of avian evolution.