Using single molecule approaches to understand DNA methylation

The establishment and maintenance of DNA methylation patterns is vital for normal development. Mutations that alter these processes not only cause human diseases but are also implicated in cancer and aging. However, our current understanding of the impact of DNA methylation in human disease is hindered by our lack of knowledge regarding the fundamental molecular mechanisms underpinning the regulation of DNA methylation. We have developed single-molecule methods to measure DNA methylation patterns using Nanopore sequencing, along with techniques to introduce synthetic epi-alleles into cells. These methods enable us to quantitatively track the evolution of DNA methylation patterns over time and examine the effects of disruptions in the DNA methylation machinery. In this PhD project, we will employ these approaches to dissect how DNA methylation is regulated within the context of chromatin and how it influences gene expression. We will conduct time-resolved inhibition and degron experiments to determine how DNA replication and chromatin re-modelling influence the establishment of DNA methylation across the cell cycle. The results of the project will help us understand how perturbation of DNA methylation leads to human disease phenotypes. We are an interdisciplinary laboratory, and the project can be approached from either an experimental or computational perspective.