Fig. 1

3D nuclear organization in candidate gene identification. a The linear organization of the genome does not provide sufficient information to predict which gene is regulated by an enhancer of interest. b Genes that are regulated by an enhancer form a 3D nuclear interaction. c The 4C-seq technique captures the 3D conformation and results in a signal around the gene that was interacting with the viewpoint (i.e. the SNP). For a detailed explanation of the 4C-seq procedure we refer to the published 4C protocol [54]. In this study, the analysis of the 3D conformation of chromatin will reveal which genes interact with an enhancer that is found at an IBD-susceptibility locus. The 4C analysis of a locus will show an interaction signal that can be mapped to the gene with which the interaction was formed. Therefore, 4C-seq can be used as a tool to use information on DNA regulation for candidate gene identification