Understanding how the genome becomes spatially organized and folded inside the nucleus is central to understanding how chromosomes function in normal development and in disease. Recent advances have shown that nuclear organization is driven by a complex collection of chromosome interactions at different genomic scales,
Cohesin plays a key role in regulating gene expression by forming DNA loops that connect genes to distal enhancers. Mutations in the structural and regulatory components of the cohesin complex lead to complex developmental disorders and cancers and are associated with chromatin misfolding and widespread gene misexpression.
Although chromosome interactions are a fundamental aspect of nuclear organization little is known about how they are established, regulated, and inherited across cell divisions. To address this gap, we developed a fully automated imaging pipeline, called HiDRO (high-throughput DNA or RNA labeling with optimized Oligopaints).