Functional analysis of constitutive heterochromatin and its relationship with oncogenic pathways

Within the nucleus, DNA is packaged with proteins into chromatin. Some parts of the genome are activated in order to produce the proteins and RNAs necessary to make and maintain different types of cells. However up to 50% of the DNA in animal genomes is comprised of repetitive DNA derived from transposable elements or invading viruses, and these regions are kept inactive by packaging them into a type of chromatin called constitutive heterochromatin. Some genes are also kept silent by constitutive heterochromatin. Given that constitutive heterochromatin occupies a substantial fraction of animal genomes, it is not surprising that its disruption affects many nuclear processes in addition to the repression of repetitive elements. Constitutive heterochromatin has both regulatory and structural roles in the nucleus, and dysfunction is associated with human disease including cancer. In addition, heterochromatin impedes the reprogramming that is necessary for the production of induced pluripotent stem (iPS) cells, which hold promise for regenerative medicine. Therefore advancing knowledge of constitutive heterochromatin is important for understanding genome regulation and disease. New knowledge has potential to identify new therapeutic targets and improve the generation of iPS cells. Despite the importance of constitutive heterochromatin in diverse areas of biology and disease, our understanding of its formation and function is extremely limited. Heterochromatin components are similar across animals, and work in model organisms has been instrumental for our current understanding of its formation and function. There is a strong history of advances made in model organisms having translational consequences in medicine, highlighting the importance of their use in basic research. Our programme will use the C. elegans model, which provides a simple but powerful system for discerning conserved mechanisms of heterochromatin formation and regulation in animals. Our programme has three distinct but interrelated aims. The first aim is to further understanding of how constitutive heterochromatin forms. We will visualise when and where heterochromatin forms in the nucleus using new super-resolution microscopy methods and by mapping the locations that heterochromatin proteins are found on DNA. We will determine the roles of heterochromatin proteins by studying strains in which they are defective and assessing the consequences of their loss. We will also investigate whether we can cause heterochromatin to form by artificially bringing different proteins to DNA. In our second aim, we will use a parallel genetic screening technique to identify a large-scale network that contains heterochromatin components, heterochromatin regulators, and proteins that are involved in causing defects when heterochromatin is not functional. We will study the functions of new genes in C. elegans and collaborate with other investigators to study shared important proteins in humans. In the third aim we will investigate the nature of the interactions between heterochomatin loss and disease pathways to help understand the abnormalities caused by heterochromatin dysfunction. We will also study whether loss of heterochromatin makes cells more receptive to abnormal signals such as those for cell division, which could increase risk of cancer or other diseases. Our programme will further our understanding of how constitutive heterochromatin forms, identify new components of heterochromatin, and determine how heterochromatin dysfunction causes pathologies. Because of the conservation of genes and biological principles across different animals, our findings might identify new biomarkers of human disease and/or therapeutic targets.