Acetylated histones at active enhancers and promoters recruit bromo and extra terminal repeats (BET) protein called BRD4. We recently demonstrated that de novo mutations in BRD4 cause a neurodevelopmental disorder called Cornelia de Lange Syndrome (CdLS) due to reduced binding of BRD4 to acetylated histones at active enhancers. The majority of neurodevelopmental disorder risk genes including BRD4 and cohesin subunits associate with enhancers, suggesting enhancer dysfunction could be a major cause of neurodevelopmental disorders. However, the mechanisms for a large number of neurodevelopmental cases remain unknown.

Building on our own publications and preliminary data, this project will aim to investigate the effect of de novo sequence variation found in neurodevelopmental disorder patients on gene expression programme and cellular phenotype in neuronal cells.

The project aims to use CRISPR Cas9 to create BRD4 mutations found in CdLS patients in human neuronal precursor cell line and investigate the effect of mutations on the altered gene expression profile in both neuronal precursor cells and differentiated neurons. Furthermore, we will analyse the effect of these mutations on histone acetylation levels at enhancers and genes that show reduced expression due to mutations by quantitative ChIPseq. We will identify the altered morphology of differentiated neurons by imaging the complexity and length of axons and dendrites, measure soma size, and we will also analyse the altered neuronal markers by immunostaining. We will then test if we can reverse the altered gene expression pattern and cellular phenotype by treating mutant cells with epigenetic drugs that increase acetylation levels for example HDAC inhibitors (HDACi) that are already in clinical trial for cancer therapy.

References

  • Olley G, Ansari M, Bengani H, Grimes GR, Rhodes J, Kriegsheim A Von, et al. Pradeepa MM and FitzPatrick D. BRD4 is mutated in a Cornelia de Lange-like syndrome and can associate with NIPBL. Nat Genet. 2018;50: 329–332. doi:10.1038/s41588-018-0042-y
  • Pradeepa MM, Grimes GR, Kumar Y, Olley G, Taylor GCA, Schneider R, et al. Histone H3 globular domain acetylation identifies a new class of enhancers. Nat Genet. 2016;48: 681–686. doi:10.1038/ng.3550

Throughout the course of the project, the successful applicant will receive comprehensive training in cutting edge genomics and bioinformatics skills. The student will also be trained on the culturing and genetic manipulation of mammalian cell lines and performing functional studies. Personalised training in writing and communication skills will be provided, complemented with generic transferable skills training from the Queen Mary Learning Institute. The student will have the opportunity to actively collaborate within and outside the research group, both at a national and international level.

Queen Mary University of London is a member of the Russell Group and is one of the leading research-focused institutions in the UK, with a large number of international students and staff. All PhD students and post-doctoral researchers are part of the Queen Mary Doctoral College, which provides support with high-quality training and career development activities. The Blizard Institute within the School of Medicine and Dentistry offers a highly interdisciplinary research environment with state-of-the-art facilities and is home to a number of research groups with core interests in genetics, epigenetics and genomics. Dr Madapura's group offers a young, vibrant and well-funded research environment, with opportunities for networking both within and outside the institution.

Applications are invited from outstanding candidates who should have, or expect to receive, a first or upper-second class honours degree in an area relevant to the project (eg Genetics, Molecular/Cellular Biology, Bioinformatics).

Interested candidates are welcome to contact Dr. Pradeepa Madapura
at p.m.madapura@qmul.ac.uk. Please include your CV, motivation letter and contact details of at least two academic referees.