The long-range interaction landscape of gene promoters

Genes can be regulated by genomic elements located far away from their transcription start sites. Despite ongoing genome-wide efforts to identify and catalog all genes and functional regulatory elements, these mapping projects do not reveal which elements control the expression of any given gene. Distant regulatory elements have been found to physically associate with target genes, and direct mapping of these looping interactions provides a means to identify elements and their respective targets. The advent of powerful chromosome conformation capture (3C) technique and its high-throughput adaptations has made it possible to detect spatial proximity and specific long-range chromatin interactions between genomic elements. We used 3C carbon copy (5C) technique to generate 'connectivity maps' of 44 ENCODE pilot project regions representing 1% of the human genome in four different cell lines including human ES cells. Based on the data, I will discuss the emerging principles of long-range interactions of gene promoters that define their functional relationship with distal elements to form complex chromatin interactome networks.