A 3C-carbon copy (5C) approach47,48 provided unbiased detection of long-range interactions with TSSs in a targeted 1% of the genome (the 44 ENCODE pilot regions) in four cell types (GM12878, K562, HeLa-S3, and H1hESC)49. We discovered hundreds of statistically significant long-range interactions in each cell type after accounting for chromatin polymer behavior and experimental variation. Pairs of interacting loci showed strong correlation between the gene expression level of the TSS and the presence of specific functional element classes such as enhancers. The average number of distal elements interacting with a TSS was 3.9, and the average number of TSSs interacting with a distal element was 2.5, indicating a complex network of interconnected chromatin. Such interwoven long-range architecture was also uncovered genome-wide using chromatin interaction analysis with paired-end tag sequencing (ChIA-PET)50 applied to identify interactions in chromatin enriched by RNA polymerase II (PolII) ChIP from five cell types51. In K562 cells, we identified 127,417 promoter-centered chromatin interactions using ChIA-PET, 98% of which were intra-chromosomal. While promoter regions of 2,324 genes were involved in “single-gene” enhancer-promoter interactions, those of 19,813 genes were involved in “multi-gene” interaction complexes spanning up to several megabases, including promoter-promoter and enhancer-promoter interactions51.
