Epigenome patterning in oocytes and its legacies in the embryo

Although we inherit 22 chromosomes from each of our parents, the egg and the sperm pass on more than the bare DNA sequence. The DNA sequence and the chromosomes themselves are modified by numerous chemical tags - call epigenetic marks - that are vital for specifying which genes should be active and which silent in any cell in our body. Where these epigenetic marks are placed on the DNA is constantly being modified as cells develop and differentiate into different tissues. It is also crucial that most epigenetic marks that were present in the egg and sperm are removed at fertilisation, so that the programme of gene expression for development of the embryo can be kick started correctly. However, some epigenetic tags can persist throughout our lifetimes, and some even remain as a permanent memory of whether a gene came from the egg or sperm. As a result of this special class of tags, some genes exhibit different activities of the copy inherited from mothers and the copy from fathers. These are referred to as "imprinted genes", because they are imprinted differently in the sperm and egg. Imprinted genes are particularly important for the normal development of the placenta and for how the fetus grows.

We are trying to understand how imprinted genes are epigenetically tagged during the development of egg cells and how these tags are remembered as the embryo develops. It seems that different types of epigenetic tags are involved - some directly on DNA, some on the chromosome structure - and some marks will end up more important in the embryo itself whereas others will be more influential in the placenta, which nonetheless can control how the baby grows and develops.

Much of the work we propose will be conducted in mouse models, where we can modify the epigenetic marks on genes, or the activity of genes, and we can access tissues - egg cells and very early embryos - in a way that we cannot do so with human samples.

Some of our work uses very sensitive techniques we have developed that can read all the epigenetic marks in individual cells. We are now using these techniques to understand if there is variation in epigenetic marks in human embryos before they implant. We believe that some differences can be traced back to the eggs from which the embryos developed, leading us to propose that some epigenetic changes could be diagnostic for problems in fertility.

Transmission of epigenetic information from parent to offspring is generally precluded by multiple genome-wide reprogramming steps that occur from the specification of germ cells, during gametogenesis, in the preimplantation embryo, and with establishment of lineage-specific epigenomes from implantation. Yet the extent to which there is inter-generational transmission of epigenetic states is still unclear and of substantial interest, eg, in relation to factors such as the increase in maternal obesity and the programming of adverse metabolic outcomes in offspring, or whether epigenetic fidelity is compromised by procedures for assisted reproduction. Genomic imprinting provides the best paradigm for epigenetic inheritance, and which is fundamentally important for normal offspring growth, development and long-term health. Until recently, it appeared that there was a single modality of imprinting, determined by gamete-derived DNA methylation, but recent studies prompt us to develop a more nuanced view and to recognise additional pathways to imprinting, such as chromatin-determined imprinting.

This programme will explore transcriptional control and how transcription patterns the epigenome in the oocyte and the legacies of these events in the embryo. It will investigate how DNA methylation-dependent and chromatin-dependent modes or imprinting are set up at different times in the female germline and how they contribute in different ways to developmental processes in the embryo and extra-embryonic lineages. It will assess general principles at the genome-wide scale, but also work at the level of specific loci to test mechanistic details and functional impacts of the different modes of imprinting. It will explore variation in DNA methylation in human preimplantation embryos, how this variation can be traced back to methylation variation in oocytes and seek to eludiate the genetic basis and pathophysiological correlates of such variation.

Our research aims to understand fundamental processes in oocytes (egg cells) by which epigenetic information is set up, and how epigenetic information is then passed on and modified in the embryo. Epigenetic information comprises the chemical tags on the DNA or the chromosomes that help demarcate active and inactive genes. In general, epigenetic information present in oocytes is erased in the early embryo to enable the embryonic gene expression programme to be properly executed, as well as to prevent transmission of epigenetic abnormalities between parents and offspring, which could be acquired as a result of environmental factors or diet. Despite the general reprogramming of epigenetic informaion, some needs to be transmitted from the egg and faithfully maintained for proper development of the fetus; this occurs at a class of genes called imprinted genes. Recent work has shown that there is an unexpected diversity of imprinted genes specified by different types of epigenetic information present in eggs: those controlled by chemical tags directly on the DNA (methylation); or those controlled by modifications on chromosome proteins (histones). We are only beginning to understand the extent and significance for normal development of these newly identified forms of imprinting. Moreover, it is still not fully understood the extent to which epigenetic information is destabilised by environmental factors or by processes associated with assisted reproduction technologies (ART). Therefore, it is imperative that further developments in ART methods that seek to improve fertility treatments are evaluated for epigenetic safety, because epigenetic errors in early development can have long-term impacts on offspring health and modify an individual's risk of disease in later life.

Much of our research will be done in a model organism, the mouse, in which these processes are most easy to investigate and because the processes are generally conserved with human. We shall also investigate the extent of epigenetic variation in human eggs and early embryos, where we believe that DNA methylation variation could be a robust molecular marker of gene expression anomalies in the ovary, and could influence the potential of the embryo for normal development.

Therefore, we expect to have impact in knowledge of the basic molecular mechanisms that govern how genes are controlled in the egg, and in the mechanisms that determine how epigenetic information is retained in the embryo to ensure correct imprinting. These advances will have wide-ranging impact in the academic community interested in mammalian developmental epigenetics and transgenerational inheritance. And they could have impact on our understanding of possible epigenetic contributions to chronic disease for which genetic causes remain ill-defined.

Our investigation of the extent and consequences of epigenetic variation in human eggs and embryos will have impact for clinicians working in reproductive medicine and for patients seeking fertility treatments, or undergoing fertility preservation.

We also expect major impact of our research in the technical capabilities we have and the advances we shall continue to make in methods for profiling epigenetic marks in very small numbers of cells or in single cells. Such advances are having widespread application in biomedical research, providing new levels of understanding of cell-fate decisions, and cell identity and function, both in normal development and physiology and in disease. We collaborate with several groups (both academic and biotech sectors) from research areas unrelated to our field who have an interest in applying these cutting-edge methods to their own biomedical questions. Therefore, we anticipate significant impact in training and knowledge exchange also at a technical level.