3D genome analysis reveals secrets to antibody diversity

Key points:

• The millions of different antibodies that help our immune system to fight infection are generated by cutting and pasting together only 200 genes in different combinations but the full picture on how this huge amount of variety is achieved has been missing.
• Researchers at the Babraham Institute have discovered a mechanism which brings together different combinations of genes into close physical proximity to generate unique antibodies in each B cell.
• Using 3D models and techniques to investigate DNA folding in B cells from mice, the scientists have shown that each antibody generating cell organises antibody DNA completely differently.  
• With further research this new mechanism may help explain changes to antibody repertoire as we age.

One of the remaining mysteries of immunology is the exact mechanism that B cells use to generate millions of antibodies with different specificities to protect us from the plethora of pathogens in the environment. Utilising research expertise in antibody variation and 3D genome organisation, researchers at the Babraham Institute have shown how unique DNA associations in each B cell lie at the heart of antibody variation. With further research, their findings could give insight into why antibody diversity declines with age and suggest interventions to address this to ensure improved health in later life.

A multi-disciplinary team of immunologists, bioinformaticians, biophysicists, and pioneers in 3D genome analysis led by Dr Anne Corcoran at the Babraham Institute have discovered that the 3D organisation of DNA in B cells from mice allows for genes that are physically far away from each other to come together during antibody generation and generate the diversity of antibodies needed for robust protection against disease. Surprisingly, they found that every B cell folds this part of the genome differently, rather than showing some conserved folding, meaning there are endless ways to combine genes into a unique order.

“We wanted to understand the mechanisms behind antibody variety. One way the cell achieves this is cutting and pasting from a suite of options for the antibody genes, but the puzzling thing is genes that are far away from the location of this event are used just as often as ones close by, so there must be some way of bringing everything together and making sure that everything needed is at hand.” explained Dr Anne Corcoran, senior group leader in the Institute’s Immunology programme.

Until now, researchers lacked the tools to investigate these mechanisms, but there were two schools of thought; one said the arrangement of DNA would be flexible and the other thought there would be common principles to the folding. Thanks to the Corcoran lab’s refined methodology, they have been able to map the chromosome interactions in high resolution for the first time and resolve the debate.

The team developed a next generation sequencing method that allowed them to gather a deeper level of DNA configuration information from B cells. The technique was a development of the enriched Hi-C genome analysis method developed at the Institute which identifies points of direct chromosomal contact across the genome at high resolution. With this enriched data set, they were able to understand more about the looping of the DNA and chromosomal interactions. The Babraham team collaborated with Dr Luca Giorgetti’s lab at the Friedrich Miescher Institute (FMI) in Basel, Switzerland, to generate 3D simulations of thousands of gene structures to validate their findings.

As well as mapping the interactions of the antibody genes, the team also found associations between key genes that support the development of B cells in a developmental stage-specific and cell type-specific way. The team suggest that these chromosomal contacts may be important for the correct and coordinated regulation of gene expression as the B cell develops.

“We found that the antibody genes were in close proximity to a small proportion of other genes on different chromosomes. Once we characterised them we found that these genes were associated with B cell development.” Dr Corcoran said, “and that was very interesting to see because if we apply this approach to other cell types we might be able to find important chromosomal interactions that are unique to those cell types.”

The team speculate that the DNA folding might influence the number of different antibodies produced by the body as we age. During ageing, our bodies make a smaller range of antibodies, as B cells select fewer genes from the available repertoire. In particular, they use fewer of the ones that are more remote. It is possible that this is due to changes to the DNA folding mechanism that mean some genes become ‘unreachable’ and are no longer selected for antibody generation.  The next steps for this research will be to investigate the 3D organisation of antibody-specifying genes in ageing B cells.

Notes

Publication reference

Mielczarek, O. et al. Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes. Cell Reports

Press contact

Dr Louisa Wood, Head of Communications, louisa.wood@babraham.ac.uk

Image description

The image shows a visual representation of the research, utilising and adapting figures from the research publication. The two background shapes illustrate chromosomal interaction mapping for two types of related techniques, showing an enrichment in the detection of chromosomal DNA interactions for the method used in this research for pro-B cells (lower shape) taken from figure 1C. The foreground shapes show the variation in DNA conformation at the immunoglobulin heavy chain locus from different pro-B cells (figure 3A in the research publication).

Affiliated authors (in author order):

Olga Mielczarek, former PhD student, Corcoran lab

Carolyn Rogers, former PhD student, Corcoran lab

Louise Matheson, postdoctoral researcher, Turner lab

Michael Stubbington, former PhD student, Corcoran lab

Stefan Schoenfelder, group leader, Epigenetics programme

Daniel Bolland, former postdoctoral researcher, Corcoran lab

Biola Javierre, former postdoctoral researcher, Fraser lab (part of the former Nuclear Dynamics research programme)

Steven Wingett, former bioinformatician in the Bioinformatics facility

Csilla Várnai, former postdoctoral researcher, Fraser lab

Anne Segonds-Pichon, former biostatistician, Bioinformatics facility

Felix Krueger, former bioinformatician in the Bioinformatics facility

Simon Andrews, Head of Bioinformatics

Peter Fraser, former group leader and Head of Nuclear Dynamics research programme

Anne Corcoran, senior group leader, Immunology research programme

Research funding

This research was supported by funding from the BBSRC, part of UKRI and the Medical Research Council.

Animal research statement

As a publicly funded research institute, the Babraham Institute is committed to engagement and transparency in all aspects of its research. The research presented mice were humanely killed for bone marrow to be collected for analysis. The techniques used in this study allowed more cells to be analysed per sample and therefore reduced the number of mice needed.

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About the Babraham Institute

The Babraham Institute undertakes world-class life sciences research to generate new knowledge of biological mechanisms underpinning ageing, development and the maintenance of health. Our research focuses on cellular signalling, gene regulation and the impact of epigenetic regulation at different stages of life. By determining how the body reacts to dietary and environmental stimuli and manages microbial and viral interactions, we aim to improve wellbeing and support healthier ageing. The Institute is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, through Institute Strategic Programme Grants and an Institute Core Capability Grant and also receives funding from other UK research councils, charitable foundations, the EU and medical charities.

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