Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome

Mutations in the DNA methyltransferase DNMT3B cause the recessive genetic condition Immunodeficiency-centromeric instability-facial anomalies syndrome type 1 (ICF1). DNMTs deposit the repressive epigenetic mark DNA methylation on the genome. However, DNMT3B is recruited to the genome through multiple pathways making it challenging to connect altered ICF1 DNA methylation patterns to disease phenotypes.

In this PhD project, we will build on our recent findings demonstrating that DNMT3B is recruited to constitutive heterochromatin through its N-terminal region (Taglini et al, 2024) to dissect the role of different DNMT3B functions in ICF1. We will generate human embryonic stem (ES) cell lines with separation-of-function mutations targeting different DNMT3B recruitment pathways before characterising their epigenome and transcriptome using Nanopore sequencing, RNA-seq and ATAC-seq. We will compare changes seen in these cells to those observed in human ES cells engineered to contain ICF1 mutations. ICF1 is characterised by craniofacial phenotypes which can be modelled by differentiating human ES cells towards neural crest cells (Prescott et al, 2015; Long et al, 2020). Therefore, to determine the effect of DNMT3B mutations on neural crest specification, we will assay differentiating embryonic stem cells using single-cell RNA-seq, ATAC-seq and Nanopore sequencing. These data will be analysed using the diffTF and GRaNIE pipelines to link changes in transcription factor activity to epigenetic and gene expression changes in DNMT3B mutants and identify affected gene-regulatory networks (Bunina et al, 2020, Kamal et al, 2023). This project will lay the groundwork for future understanding the molecular basis of ICF1 patient phenotypes and ultimately the rational designing of therapeutic approaches.

The project is a collaboration between the Sproul and Long groups (MRC Human Genetics Unit, University of Edinburgh) with the Bunina group (Max Delbruck Centre, Berlin). It would ideally suit those with a backgrounds in human genetic disease, gene regulation, chromatin, epigenetics and the application of quantitative approaches to biology. Applicants with other training backgrounds who are motivated to learn the necessary background and skills will also be considered.

• Bunina et al 2020 Cell Systems 10:480-494
• Kamal et al 2023 Molecular Systems Biology 19:e11627
• Long et al 2020 Cell Stem Cell 27:765-783
• Prescott et al 2015 Cell 163:68-83
• Taglini et al 2024 EMBO Reports 25:1130-1155

For informal enquiries about this project, please contact Duncan Sproul D.sproul@ed.ac.uk