About the Project
Please click on the Babraham Graduate Programme button above for details of how to apply for this project.
Our lab studies the epigenetic mechanisms that drive antibody recombination to generate the diverse antibody repertoire we need to fight infection. These include nuclear organisation and local and long-range chromatin states. We also study defects in these processes that cause leukaemias, and immunodeficiencies, including ageing. We are collaborating with a Cambridge company that has a mouse model with a human immunoglobulin locus, which offers the unique opportunity to study human antibody recombination and its underpinning epigenetic mechanisms in a tractable mouse model, a major advance on limited studies in human bone marrow. We have recently developed next generation sequencing methods to analyse recombination frequency (VDJ-seq) and associated local chromatin states (Bolland et al 2016; Chovanec et al, in press; Matheson et al, under review), as well as regulation of immunoglobulin recombination by 3D DNA looping and genome-wide interactions in mouse B cells (Mielczarek et al, in prep). This project will apply these techniques to the human system. First, VDJ-seq analysis of the human Igh transgene antibody repertoire will be integrated with chromatin immunoprecipitation (ChIP-seq) datasets for relevant factors and histone modifications, to discover the local chromatin signatures that drive recombination of human Igh genes. This will both illuminate local epigenetic regulation of human V(D)J recombination, and identify chromatin signatures that may reveal genome-wide off-target recombination sites that lead to chromosomal translocations and leukaemias. Parallel experiments will be conducted in human bone marrow samples. Second, this project will determine how the human Igh locus is folded in 3D nuclear space to bring genes together for recombination, and whether and how it interacts with other important regions of the genome to regulate B cell development. Recent advances in chromosome conformation capture (3C) techniques have enabled detection of the interactions of every DNA element with every other element and this allows us to determine which genes are in proximity to the immunoglobulin loci. The project will develop Capture HiC for the human Igh to reveal cis interactions, DNA looping structures and new regulatory elements required for recombination within the human Igh locus, both in the mouse transgene model, and in human bone marrow progenitor B cells. Interactions of the Ig loci in trans will be interrogated to discover interchromosomal interactions that drive both normal human B cell development, and increase susceptibility to chromosomal translocation. Together these experiments will provide the first comprehensive insight into local and global epigenetic mechanisms underpinning human antibody recombination, identify genome-wide sites of aberrant recombination, and improve future rational design of human Ig transgene platforms, the next generation of therapeutic humanised antibodies. Techniques including next generation sequencing, bioinformatics and flow cytometry are all well-established in the lab and the project will also include a short placement with the company.
For more information, please visit our website:
http://www.babraham.ac.uk/our-research/nuclear-dynamics/anne-corcoran
or contact Anne Corcoran: [Email Address Removed]
References
Bolland, D.J, Koohy, H., Wood, A.L., Matheson, L.S., Krueger, F., Stubbington, M.J.T., Baizan-Edge, A., Chovanec, P., Stubbs, B.A., Tabbada, K., Andrews, S.R., Spivakov, M., and Corcoran, A.E. (2016) Two mutually exclusive local chromatin states drive efficient V(D)J recombination. Cell Reports 15: 2475-87
Stubbington, MJT and Corcoran, AE. (2013) Non-coding transcription and large-scale nuclear organisation of immunoglobulin recombination Curr Opin Genet Dev 23: 81-88