The study investigates the long-range interactions between gene promoters and distal regulatory elements in the human genome using chromosome conformation capture carbon copy (5C). The researchers applied 5C to 1% of the human genome, representing 44 ENCODE pilot project regions, in three cell lines: GM12878, K562, and HeLa-S3. They identified over 1,000 long-range interactions between promoters and distal sites, including elements resembling enhancers, promoters, and CTCF-bound sites. The results showed significant correlations between gene expression, promoter-enhancer interactions, and the presence of enhancer RNAs. Long-range interactions were found to be asymmetric, with a bias for interactions with elements located ~120 kilobases upstream of the transcription start site (TSS). These interactions were often not blocked by CTCF and cohesin, indicating that many sites do not demarcate physically insulated gene domains. Additionally, only about 7% of looping interactions involved the nearest gene, suggesting that genomic proximity is not a simple predictor for long-range interactions. The study also revealed that promoters and distal elements form complex networks, providing insights into the three-dimensional context of genes and regulatory elements.The study investigates the long-range interactions between gene promoters and distal regulatory elements in the human genome using chromosome conformation capture carbon copy (5C). The researchers applied 5C to 1% of the human genome, representing 44 ENCODE pilot project regions, in three cell lines: GM12878, K562, and HeLa-S3. They identified over 1,000 long-range interactions between promoters and distal sites, including elements resembling enhancers, promoters, and CTCF-bound sites. The results showed significant correlations between gene expression, promoter-enhancer interactions, and the presence of enhancer RNAs. Long-range interactions were found to be asymmetric, with a bias for interactions with elements located ~120 kilobases upstream of the transcription start site (TSS). These interactions were often not blocked by CTCF and cohesin, indicating that many sites do not demarcate physically insulated gene domains. Additionally, only about 7% of looping interactions involved the nearest gene, suggesting that genomic proximity is not a simple predictor for long-range interactions. The study also revealed that promoters and distal elements form complex networks, providing insights into the three-dimensional context of genes and regulatory elements.