Dissecting DNMT3B functions in human development

Department: Institute of Genetics and Cancer

Number of current Students: 1 in 4th year (MRC HGU DTP)

Completed Supervisor training: Completed

Co Supervisors: Hannah Long, Institute of Genetics and Cancer, University of Edinburgh (hannah.long@ed.ac.uk) / Marcus Wilson, School of Biological Sciences, University of Edinburgh (marcus.wilson@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 cause disease. However, we do not currently understand why DNA methylation defects cause abnormal development.

DNA methylation is patterned by DNA methyltransferase enzymes (DNMTs) which are recruited and regulated by multiple pathways. Our recent work has dissected and defined these pathways providing the opportunity to understand which DNMT functions are required for development to proceed correctly.

This project focuses on dissecting the role of DNMT3B, the enzyme primarily responsible for methylating the genome during early development. DNMT3B knockout is lethal in mice and human mutations cause the recessive genetic developmental condition Immunodeficiency centromeric instability facial anomalies syndrome type 1 (ICF1) (Rolls et al 2024). We have recently delineated a novel pathway recruiting DNMT3B to constitutive heterochromatin (Taglini et al, 2024).

To understand why DNMT3B is critical for development, we will generate human embryonic stem cell (hESC) lines with separation-of-function mutations targeting different DNMT3B recruitment pathways before characterising their epigenomes and transcriptomes. We will then differentiate these hESC lines to understand how DNMT3B defects impact on development. As DNMT3B mutations affect facial patterning in ICF1, we will focus on differentiating hESCs to cranial neural crest which are a key cell type for facial patterning (Long et al, 2020). This project lays the groundwork to understand the molecular basis of why correct DNA methylation patterning is vital for human development.

The project is a close collaboration between the Sproul, Long and Wilson groups at the University of Edinburgh. The successful applicant will work within the vibrant, interdisciplinary research community at the 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. During the PhD, the student will gain experience in hESC culture, genome editing, Nanopore sequencing, CUT&Run, scRNA-seq and computational analysis of the resulting data.

• Long et al 2020, Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder - ScienceDirect
• Rolls et al 2024, Using human disease mutations to understand de novo DNA methyltransferase function | Biochemical Society Transactions | Portland Press
• Taglini et al 2024, https://doi.org/10.1038/s44319-024-00061-5

BBSRC Remit Area: Understanding the Rules of Life (within Advancing the Frontiers of Bioscience Discovery)