4D Genome Architecture, Gene Regulation & Developmental Disease
Most developmentally important genes have complex and pleiotropic expression patterns. Such spatially and temporally restricted transcriptional activities are largely controlled by cis-regulatory elements such as enhancers that can be far away from their target gene. Our current knowledge how enhancers activate their target genes is limited. How genes are regulated and how this works within the nuclear space remains elusive and is probably some of the biggest challenges in the post-genomic era.
The folding of chromosomes in the nucleus is tightly controlled. This folding process has a dual role, it compacts the genomic information within the nucleus and, at the same time, has an important role in gene regulation. Studies using technologies such as HiC have shown that the genome is partitioned into megabase scale compartments called topologically associated domains (TADs). Because TADs restrict the range of enhancer targets, enhancers usually contact genes located within these TADs, but not outside. TADs have been shown to be surprisingly stable across cells, tissues and even species, suggesting that they function as a general folding scaffold determining domains of possible interaction partners. We previously showed that deletions, duplications, inversions, translocations and insertions, collectively called structural variations (SVs), can result in disease-causing rewiring of enhancer-promoter contacts by changing the TAD configuration at a locus.
Using primarily mouse limb development as a model system, we investigate how changes in 3D genome organization impact on gene regulation during development and disease. We are interested in fundamental principles of enhancer-mediated gene regulation and the rewiring of 3D architecture by SVs. In addition, we investigate the role of long-non-coding RNAs and transposable elements in gene regulation, 3D genome organisation and developmental disorders. To accomplish this, we are using a large variety of state-of-the-art technologies: on the one hand, we employ Chromosomal Conformation Capture technologies (4C, Hi-C), ChIP-seq, and RNA-seq to describe regulatory landscapes. On the other hand, we apply CRISPR-Cas9 genome editing to induce various genetic re-arrangements (deletions, inversions, duplications, insertions) and study their impact on chromatin architecture, gene regulation, and limb development.