Genome Architecture Mapping: discovering 3D genome topology in rare cell types
The folding of chromosomes and the structural organization of the genome impacts human health and disease. Long-range physical contacts between non-coding regulatory regions and their target genes regulate gene expression. In dividing cells, chromatin contacts are established when cells exit mitosis to dissolve upon re-entry into mitosis. We set out to investigate the functional relevance of chromatin contacts in terminally differentiated cells, such as neurons, which retain their physiology for years in living animals. We applied a novel ligation-free technique to map chromatin contacts genome-wide Genome Architecture Mapping (GAM) which is ideally suited to study rare cell types. GAM extracts spatial information by sequencing the DNA content from a large collection of randomly orientated, thin nuclear sections, before quantifying the frequency of locus co-segregation. By applying GAM to mouse embryonic stem cells, we had previously identified specific chromatin contacts enriched for interactions between active genes and enhancers spanning large genomic distances. We have now developed faster and more affordable versions of GAM, which are compatible with their application in specific rare cell types without tissue disruption. As a proof-of principle, we have used GAM to map chromatin contacts genome-wide in specific neuronal subtypes directly from mouse brain. Our work shows that genome architecture is highly cell-type specific and reflects cell-type specific gene expression patterns at both short and long genomic distances.
Ana Pombo investigates how the 3D folding of chromosomes influences gene expression in mammalian development and disease, and epigenetic mechanisms that prime genes for future activation. She received her DPhil from University of Oxford (1998, UK) where she identified transcription factories in mammalian nuclei. She was awarded a Royal Society Dorothy Hodgkin Fellowship (UK; 1998-2002), and started leading her research group in 2000 at the MRC London Institute for Medical Sciences, Imperial College London (UK). Her laboratory moved to the Berlin Institute for Medical Systems Biology, at the Max Delbrueck Center (Berlin, Germany) in 2013, and she was appointed Professor (W3) at Humboldt University of Berlin.
Her lab has made many important contributions. They showed that human chromosomes intermingle with each other, promoting specific patterns of chromosomal translocations. They were the first to identify unusual RNA polymerase II complexes at genes regulated by Polycomb repressor complexes, which are epigenetic enzymes essential for cell lineage commitment. She has recently combined epigenomics, physics modelling and high-resolution imaging to show the importance of long-range genomic contacts between active genes and poised genes, which persist throughout the cell cycle. She has developed Genome Architecture Mapping (GAM), an exquisite technology to map the 3D structure of chromosomes genome-wide which has unique advantages. Her lab has shown that active genes and enhancers form the most specific chromatin contacts, including previously unappreciated complex three-way contacts between super-enhancers, which span the length of whole chromosomes. GAM is uniquely powerful to quantify the higher-order complexity of 3D genome and the study of rare cell types directly from tissue, including precious human biopsies. These developments open a huge field of potential applications to identify the genes affected by disease-associated genetic variants present in non-coding parts of the genome, through long-range chromatin contacts.