Researchers have developed and used a new technique to connect the dots in the genomic puzzle. Just as dots have to be connected to visualize a full picture, the researchers connected regulatory elements called promoters and enhancers and showed their physical interactions over long distances within the mouse and human genomes.

The ability to map promoter-enhancer interactions in the human genome has huge potential in understanding the genetic basis of disease.

Our development as an embryo and the establishment of different cell types in the body is dependent on a suite of genomic regulatory elements to orchestrate the correct expression of genes in different locations and at different times. To have a complete understanding of how a gene is regulated, both in health and disease, it is necessary to have a comprehensive catalogue of the regulatory elements that contribute to its control.

Researchers at the Babraham Institute and the Francis Crick Institute  refined an existing technique to look at the one million regulatory elements in the mouse genome and link these to gene promoters to understand how genes are switched on and off. At the same time, the technique was used to study human blood cell types.

If the genome is imagined as a linear stretch of DNA sequence, the research pinpointed sections of the genome where it loops to bring regulatory elements controlling gene expression into physical contact with each other. In genomic distances, enhancer regions can be hundreds of kilobases of DNA letters (1KB is 1000 letters or bases) away from the genes they regulate.

Previous interaction assays weren't able to provide sufficient resolution to link regulatory elements with specific promoters. To solve this problem, the team used using RNA 'baits' to be able to pull out just the genomic fragments containing promoters from the melting pot of a hundred billion (1011) genomic interactions in the mouse genome. The technique is called Promoter Capture Hi-C. The research served as a proof of principle for the use of Promoter Capture Hi-C to map genomic interactions in mouse cells at high resolution and the new study is the most extensive genome-wide map of promoter-enhancer interactions in the human genome. 

Use of the Promoter Capture Hi-C technique to delve the human genome pinpointed the long-range interactions of nearly 22,000 promoters, identifying millions of interactions and providing an unprecedented snapshot of the distal genomic regions that contact promoters. Genome-wide association studies have uncovered thousands of specific areas of the genome (loci) that have been shown to be associated with different diseases, including within regulatory regions. Knowing which genes a regulatory region affects has so far been extremely difficult and this has been a major roadblock to understanding genome-wide association studies.

The resolution allowed by Promoter Capture Hi-C showed that the regions that interact with promoters are highly enriched for DNA mutations (SNPs; single nucleotide polymorphisms) that have been associated with disease and means that researchers can now link potentially defective regulatory elements of the genome with the genes they influence.

Published in Nature Genetics. Funding support for this research was provided by the Biotechnology and Biological Science Research Council (BBSRC) and Medical Research Council (MRC) to Dr Peter Fraser, Leukaemia&Lymphoma Research to Dr Cameron Osborne and the European Commission to Dr Nicholas Luscombe as part of the FP7 Epigenesys network of excellence. An international patent (patent number PCT/GB2014/052664) on the Promoter Capture Hi-C technique has been submitted.