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 FISH-based imaging pipeline, called Hi-FISH, to quantitatively determine the position and interaction frequency of multiple loci in the nucleus. 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 potential of Hi-FISH by conducting the first FISH-based whole-genome RNAi screen for somatic pairing factors in Drosophila, using their well-established capacity to form these interactions as a model for chromosome interactions in general. Collectively, we isolated 105 cellular factors, many of which not previously implicated in genome organization. We are currently characterizing the function of these candidates and are also further enhancing our Hi-FISH method to screen for additional features of nuclear organization.