Epigenetic reprogramming in mammalian development. (360G-Wellcome-095645_Z_11_Z)

The main aim of my research is to understand the properties and mechanisms of genome-wide epigenetic reprogramming in the mammalian germ line, and to explore its biological and medical impacts. The key questions that I wish to address in this programme of work are firstly, what are the mechanisms of epigenetic reprogramming, and especially of demethylation of DNA? We will investigate passive and active mechanisms of erasure of methylation, including the roles played by DNA methylases, AID/APOBEC deaminases, TET hydroxylases, and the base excision repair pathway. We would like to know how these proteins are targeted to the genome during reprogramming. Second, I would like to understand the epigenomics of reprogramming as well as its biological purposes. We will determine what epigenetic information is erased in the germ line and what information is resistant to erasure, potentially resulting in transgenerational epigenetic inheritance. We are interested in how retrotransposons are p revented from mobilizing in the germ line in the face of loss of major repressive epigenetic marks that normally keep them silent. We also hope to understand how reprogramming gives rise to the stochastic patterns of gene expression that appear to be characteristic of the pluripotent state. And third, how can we apply insights into reprogramming to other areas of biology and to medicine? I expect that our insights will help to improve approaches to stem cell and regenerative medicine, with e pigenetic barriers being recognized as critical for the efficient derivation of ground state iPS cells. Also, we will create mouse models in which transgenerational epigenetic inheritance is altered which will illuminate how accumulation of epialleles might be associated with ageing and chronic diseases in humans. Our key approaches to these questions are based on epigenomics techniques, especially on small cell numbers, combined with in vivo genetic manipulation, and complemented by work on mul tipotent stem cell lines such as ES, TS, epiSC, and iPS cells which we can manipulate through knockouts or a stable inducible shRNA knockdown system.