Abstract
Sift through metadata. Track contact activity. Identify suspicious patterns. This to-do list sounds as though it were devised by the National Security Agency. But it actually describes a research plan enacted by a group of genomic scientists in Japan and the United Kingdom.
The scientists sifted through a catalogue of gene-promoter interactions, tracked promoters associated with known mutations, and identified potential “bad actors.” In this case, the suspects had nothing to do with threats to national security. Instead, they were thought to instigate disease processes, specifically, inflammatory bowel disorders such as Crohn's disease.
The scientists used technology that advances genomic surveillance as dramatically as computer networking has advanced intelligence operations, which long ago progressed from the selective planting of “bugs” and phone line “taps.” In fact, the scientists themselves likened their work to the collection and analysis of telephony metadata. The analysis of genomic metadata, the scientists suggested, will be needed if the genome is to be more useful than a mere phonebook.
“We had the phonebook, and we knew people listed in it were making calls. But we didn't know who was calling who—now we do,” said Filipe Tavares-Cadete, one of the scientists. Dr. Tavares-Cadete, a researcher at Okinawa Institute of Science and Technology Graduate University (OIST) in Japan, worked with colleagues at the Francis Crick Institute, King's College London, and the Babraham Institute to examine the long-range interactions of almost 22,000 promoters in two human blood cell types. Using Capture Hi-C (CHi-C), an adapted genome conformation assay, the scientists identified over 1.6 million shared and cell-type-restricted interactions spanning hundreds of kilobases between promoters and distal loci.
OIST
As these numbers indicate, the genome is making a lot of long-distance calls. More than half of the interactions were between promoters and sections of DNA that are very far away in the linear sequence, at least 150,000 base pairs. This is because inside the cell, DNA is tightly bundled up in loops, an arrangement that can bring bits of DNA close together even if they may appear to be extremely far apart, if they are seen as letters printed out in a line.
Long-range promoter interactions are particularly interesting for disease studies. Often DNA mutations, known as single nucleotide polymorphisms (SNPs), are located in what appears in the linear sequence as the middle of nowhere—outside, and often quite far from, genes. This makes it difficult for scientists to determine which genes the mutations affect, and thus which genes are associated with a particular disease.
By looking at which promoters interact with known SNPs, the researchers successfully identified genes known to be involved in inflammatory bowel disorders. These results appeared in Nature Genetics, in an article entitled, “Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.” The article also indicated that the mapping of long-range contacts could provide new insights and accessible tools to dissect the regulatory interactions that underlie normal and aberrant gene regulation.
“The Hi-C method simultaneously captures all genomic interactions, which provides a population-average snapshot of the genome conformation within a single experiment; yet, owing to the enormous complexity of Hi-C libraries, it is costly to sequence to sufficient depth to provide enough spatial resolution to interrogate specific contacts between gene promoters and distal regulatory elements,” the authors of the Nature Genetics article wrote. “To circumvent these issues, we have used solution hybridization selection to enrich Hi-C libraries for genome-wide, long-range contacts of both active and inactive promoters.”
This method, the scientists asserted, helps investigators delve into how networks of interactions cooperate to regulate genes. “It's really just the beginning,” said Dr. Caermon Osborne, a geneticist at King's College London. “Every type of cell will. Have its own unique set of interactions.”
While analyzing their processed metadata, the scientists also discovered new elements for turning genes off. That is, in addition to cataloguing long-distance “on” switches, enhancers, the scientists found long-distance “off” switches, silencers. The scientists noticed the long-range silencers while looking at promoters interacting with repressive histones.
“We suspect more of these long-range silencers are contacting promoters and turning off gene expression,” said Dr. Tavares-Cadete. “This underscores the major impact promoter interactions can have on the proper functioning of the genome.”