Next Generation Sequencing High Throughput Epigenomics

Recent evidence suggests that an adult individual?s health and susceptibility to common diseases can sometimes be traced back to environmental and nutritional effects experienced by their mothers or grandmothers during pregnancy. The ?experiences? of the foetus during development in its mother?s womb appears to alter the way that an individuals genome is interpreted in later life leading to, in some cases, increase susceptibility to certain diseases. This altered genome interpretation can in some cases be passed passed on to the next generation as well, even in the absence of the original conditions. Though we have the sequence of the entire human genome, we know little about how it works, and how it is interpreted by cells. In this project we will take advantage of recent breakthroughs in DNA sequencing technologies that will permit us to collect hugely increased amounts of data from the genomes of cells before, during and after development. In addition to revealing important information about the workings of the genome these results will provide important insights into the fetal origins of adult disease and potentially lead to new strategies for prevention and new medicines or therapies for treatment of conditions that affect the quality of life.

Development is the result of changes in gene expression programmes that give rise to different organs and tissues. With few exceptions, these changes occur without changes to DNA sequence. Changes in epigenetic modifications such as DNA methylation, histone modifications, histone variant deposition and the presence of non-nucleosomal chromatin-associated proteins are strongly linked to the transitions from totipotent to pluripotent stem cells, and precursor cells to fully differentiated somatic cells. Little is known about these interlaced systems work and interact. In this Collaboration Grant we propose to bring together a pre-eminent group of UK scientists working on epigenetics and chromatin during development. Our current funded research programmes are aimed at various and extensive epigenetic analyses of diverse ?developmental? cell-types; including primordial germ cells, developing oocytes, ES cells, blastocysts, TS cells, placenta, fetal liver and adult tissues. Presently these analyses are to be performed with real-time PCR, Sequenom massarray, or microarray based profiling, etc. Each of these techniques is limiting, either in terms of the number of samples or datapoints that can be assessed (PCR and Sequenom) or in the quality and quantitative value of data returned (array techniques). Rather than simply focussing on own little parts of the genome we propose to collaborate in the establishment of a new facility, to take advantage of improvements in DNA sequencing technology to create a database of genome-wide datasets representing an epigenetic time course through development. With the aid of an Illumina Genome Analyzer II (Solexa) massively parallel sequencing system we will generate genome-wide datasets for each experiment, rather than a tiny fragment of the genome. This will allow us to investigate the specific questions outlined in our present research programmes, while at the same time dramatically increasing the output and quality of each experiment. The data from each of the applicants will be deposited in a searchable database curated by the proposed postdoc. The net effect will be to create a programme that is substantially larger, more encompassing and providing much greater insight than the sum of the previous constituent parts. This collaborative database will foster interaction and sharing of expertise between applicants as well as create a shared resource for collaborative publications that would not have been possible without this grant.