RT Journal Article SR Electronic T1 The interdependent nature of multi-loci associations can be revealed by 4C-Seq JF bioRxiv FD Cold Spring Harbor Laboratory SP 028555 DO 10.1101/028555 A1 Tingting Jiang A1 Ramya Raviram A1 Pedro P. Rocha A1 Valentina Snetkova A1 Charlotte Proudhon A1 Sana Badri A1 Richard Bonneau A1 Jane A. Skok A1 Yuval Kluger YR 2015 UL http://biorxiv.org/content/early/2015/10/12/028555.abstract AB 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.