Chromosomes form local structures such as gene loops, but the influence of these structures on transcriptional regulation is not fully understood. Now, Keji Zhao, Richard Young and colleagues report the identification of chromosome structures, called insulated neighborhoods, that regulate the expression of local genes in embryonic stem cells (ESCs) (Cell 159, 374–387, 2014). The authors used cohesin chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), which maps DNA-DNA interactions at cohesin-occupied sites. Cohesin is known to associate with enhancer-promoter loops and with CTCF-bound regions. Accordingly, the authors found that 92% of interacting cohesin-occupied sites occurred at enhancers, promoters and CTCF-binding sites. They identified a structure consisting of a loop formed by two interacting CTCF sites co-occupied by cohesin that was associated with enhancers, in particular, super-enhancers that regulate the expression of key cell identity genes, and with repressed lineage-specifying genes that are marked by trimethylation of histone H3 at lysine 27 (H3K27me3). They showed that deletion of CTCF sites at five key ESC genes led to the altered expression of nearby genes, providing evidence that these structures have a functional role. The authors suggest that association of enhancers and target genes in insulated neighborhoods might have a role in preventing off-target effects.