To identity enhancer targets, DNA fluorescence in situ hybridization (FISH) [59,60], as well as chromatin association methods (chromosome conformation capture (3C)) [61], can be employed. These are powerful approaches for evaluating whether a region of interest interacts with a specific genomic target, but they suffer from the limitation that the regions of interest must be pre-specified, that is, they are ‘one-by-one’ approaches. 4C (circular chromosome conformation capture), an extension of 3C, can capture all regions that physically contact a site of interest, without prior knowledge of the regions that contact that site being necessary [62] (that is, a ‘one-to-all’ approach). Higher-throughput methods include carbon-copy chromosome conformation capture (5C, many-to-many), a high-throughput expansion of 3C, Hi-C (all-to-all) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) (for detailed comparison of these methods, see reviews [63,64]). These global approaches can enable the identification of loci that directly and indirectly contact enhancers of interest, and can reveal complex interactions in which dozens to hundreds of loci aggregate, so-called transcriptional hubs or enhanceosomes [65]. These types of high-order interactions have been recently described by
