The interdependent nature of multi-loci associations can be revealed by 4C-Seq

Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that these associations act in isolation of other interacting partners within the genome. Indeed, the influence of multi-loci interactions in gene control remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise interactions involving the Tcrb and Igk antigen receptor enhancers, in addition to novel tri-loci associations. We further show that enhancer deletions not only interfere with tri-loci interactions in which they participate, but they also disrupt pairwise interactions between other partner enhancers and this disruption is linked to a reduction in their transcriptional output. These findings underscore the functional importance of hubs and provide new insight into chromatin organization as a whole. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings.