講演情報
[S9-2]Structural variants in the light of 3D genomics - how abnormal gene regulation can cause disease
○Stefan Mundlos1,2 (1.Max Planck Institute for Molecular Genetics, Berlin, Germany, 2.Charité, Universitätsmedizin Berlin, Berlin, Germany)
Recent studies have shown that the genome shows a specific three-dimensional organization in the nucleus which has a major influence on gene regulation. Mammalian genomes are organized in distinctly folded chromatin modules, called topologically associated domains (TADs) that are separated from each other by boundary regions. TADs subdivide the genome into discrete genomic units that restrict the possible contacts enhancers can establish with their target genes. We use a CRISPR/Cas9 based strategy to investigate the effect of human disease-associated structural variations in vivo in mice. We show that deletions can result in the fusion of TADs and the re-wiring of enhancer-promoter contacts. At the EPHA4 locus, for example, deletion of parts of the TAD including the boundary result in the activation of the nearby Pax3 gene by Epha4 enhancers and a limb malformation. Furthermore, we analyzed overlapping duplications at the SOX9 locus, that are associated either with a limb malformation (Cooks syndrome), sex reversal, or no abnormality. We show that large duplications spanning a TAD boundary result in the formation of a novel TAD, or neo-TAD. However, the loss of TAD structures induced by cohesin or CTCF depletion results in only modest changes in gene expression questioning the importance of TADs in regulating gene expression. In a further series of experiments, we analyzed the function TADs and their boundaries in vivo in the context of limb development. At the Sox9 locus we removed all CTCF sites at the boundary and within the two flanking TADs, one containing Sox9, and the other Kcnj2. We show that TADs and their CTCF directed loops provide precision and robustness to developmental gene expression but enhancers can find their target genes without them. If enhancers are redirected by CTCF, however, they can activate the wrong target gene, induce misexpression and ultimately cause disease. Our findings provide a framework for interpreting the pathogenic effect of structural variations, which are frequently detected in patients with congenital malformations, intellectual disability and cancer.