Dissecting the effects of gene body methylation on gene expression in mammals

• d.sproul@ed.ac.uk
• grzegorz.kudla@ed.ac.uk

DNA methylation is a repressive epigenetic mark whose genomic pattern is established early in mammalian development. The correct patterning and maintenance of DNA methylation is vital for development to proceed normally, and disruptions are associated with disease and aging.

DNA methylation is most frequently regarded as exerting its primary effect through the repression of promoters (1). However, mammalian gene bodies are also methylated, even though it entails the deposition of mutagenic DNA methylation within the coding sequences of genes. Gene body methylation is also conserved across the tree of life to a greater degree than promoter methylation (2). Taken together, this suggests it plays an important role in gene regulation. Previous work has led to suggestions that gene body methylation promotes transcription by repressing spurious initiation from cryptic promoters or regulating splicing, however it remains poorly understood (1).

We have recently developed a synthetic approach to directly test the impact of gene body methylation on gene expression in mammalian cells. Here we will combine this with high-throughput analyses of synthetic gene variants (3) and CRISPR perturbation experiments to delineate the mechanisms through which gene body methylation affects gene expression. We will also use quantitative computational analyses of functional genomics data to determine how the requirement for these factors varies across genes in the genome. During the PhD, the student will gain experience in cell culture, synthetic biology approaches, CRISPR screening, and computational analyses. Having uncovered factors that mediate the effects of gene body methylation on gene expression, they will dissect the mechanisms through which they mediate their effects using genetic, molecular biology and biochemical approaches (eg CRISPR knock-in, IP-mass spectrometry).

The project is a collaboration between the Sproul and Kudla groups at the University of Edinburgh’s Institute of Genetics and Cancer. The successful applicant will work within the vibrant, interdisciplinary research community at Institute of Genetics and Cancer. It would ideally suit those with a strong interest and background in gene regulation, chromatin and epigenetics with quantitative skills. Applicants with other training backgrounds who are motivated to learn the necessary skills will also be considered.

References:

1. Greenberg et al 2019 Nature Reviews Molecular Cell Biology 20:590–607 DOI: 10.1038/s41580-019-0159-6
2. de Mendoza et al 2020 Journal of Molecular Biology, 432:1687-1705 DOI: 10.1016/j.jmb.2019.11.003
3. Mordstein et al 2020 Cell Systems DOI: 10.1016/j.cels.2020.03.001