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).
HiDRO permits quantitative measurement of chromatin interactions across a large number of samples. This technique enables us to image thousands of cells and use special statistical methods to determine whether and to what extent a variable (RNAi, CRISPR, drug, etc) alters chromosome organization and function. Recently, we have shown the utility of HiDRO by conducting the first large-scale FISH-based screen for looping factors in Human cells. We screened the human druggable genome and identified ~300 factors that regulate chromatin folding during interphase, including 43 validated hits that either increase or decrease interactions between topological associating domains (TADs). These results connect major signaling pathways to nuclear architecture and underscore the broader utility of HiDRO-based screening to identify novel mechanisms that drive the spatial organization of the genome.