The functional requirement for epigenetic systems in development and disease

Exposure to environmental factors e.g. tobacco smoke, chemicals, air pollutants and nutrition can adversely affect human health. This can result in alterations to ‘chemical tags’ which normally exist on our DNA. These tags correspond to 'epigenetic marks'(on top of DNA) that can act as a ‘barcode’ of DNA function by indicating if genes are in an active or silent barcode state. Variations in the barcode can represent environmental induced changes in gene expression that have downstream adverse effects on the way cells and tissues work. This may result in enhanced disease susceptibility, for example resulting in an increase in cancer incidence or be linked with premature ageing processes.

In this project we will study the contribution of epigenetic marks in regulating gene expression. Embryonic stem cells (ESCs) are models for early mouse development that can be grown in a petri dish under different culture conditions that either promote their continuous regeneration or alternatively coax them to differentiate into specific tissue types such as neural tissue. Of great interest is that one the chemical tags, 5-methylcytosine (5mC), undergoes programmed changes that are indicative of differentiation state and gene expression profiles. We will study how the lack of key enzymes (DNA methyltransferases (Dnmts)), which are important in DNA methylation reprogramming, affects ESC differentiation. Using appropriate model systems, we will undertake a detailed analysis to determine how lack of the Dnmt enzymes alters the ability of cells to differentiate normally. We use high resolution molecular profiling and imaging techniques to gain a better understanding of the contribution of epigenetics to development and by implication disease states. These studies underpin the new development of powerful diagnostic tests for disease, provide new markers for monitoring environmental exposure and promote the development of novel therapeutic interventions.

Epigenetics can be defined as an alteration in gene activity that is mitotically stable in the absence of a change in DNA sequence. In practice it represents a combination of observations and suggested mechanisms that are thought to functionally organize the genome to regulate gene expression, preserve genome integrity, propagate cell identity and govern transcriptional responses to external stimuli. Our aim is to determine the molecular mechanisms of epigenetic gene regulation that are associated with DNA modification in development and by implication in disease model systems Recent work (including our own) in mouse embryonic stem cells (ESCs) suggests that signal transduction pathways determine epigenetic states and not vice-versa. Most surprisingly we find that cell transition states in ESCs (primed to ground state and vice versa) are independent of global DNA methylation status. This work resulted in system with which we can directly investigate the mechanisms involved in over-riding the repressive effects of DNA methylation at target promoters, which will have important implications for understanding how activation and silencing of DNA methylated genes (and endogenous retroviruses (ERVs)) occurs in development and disease. Our previous analysis suggested that general aberrant promoter hypermethylation in cancer does not necessarily directly promote tumorigenesis, but instead reinforces transcription repression inherited from pre-cancerous tissue. Our work in ESCs has led us to develop new models to explain the molecular basis of this observation, which potentially de-links de novo methylation of promoters as a direct driver of disease processes and perhaps physiologic states (ageing). We have also observed that global DNA methylation states impacts on Polycomb Repression Complexes (PRC1 and 2) dependent chromatin compaction in the nucleus of embryonic stems cells (ESCs). Currently we are investigating the molecular models involved in facilitating DNA methylation directed changes in higher order chromatin organisation and its relevance to developmental gene regulation. We use various ESC models and in vitro models for early development to address how defects in defined aspects of the DNA methylation machinery influence the transition of stem cells to more committed cell fates. Increased understanding of these basic processes underpins the interpretation and relevance of altered epigenetic profiles in disease, ageing, drug screening programs and environmental exposure.