New Method for 3D Mapping of the Genome

March 9, 2017
New Method for 3D Mapping of the Genome
Top: Diagram with red coding for sequences that are close by, blue coding sequences further apart. Gene switch (enhancer, E) is close to gene Y but not gene X. Bottom: Position in the nucleus. [Pombo Lab, MDC]

An international team of researchers led by investigators at the Max Delbrück Center for Molecular Medicine in The Helmholtz Association (MDC) and the University of Napoli has just developed a powerful new technique that “maps” the 3D geography of the entire genome. Findings from the new study were published recently in Nature through an article entitled “Complex multi-enhancer contacts captured by genome architecture mapping.”

The new technique called Genome Architecture Mapping, or GAM, helps to identify gene contact regions. This method involves flash-freezing tissue or cells, then cutting thin slices of individual nuclei. The tiny amount of DNA within each slice of the nucleus is then sequenced, and the team deploys a mathematical model, named SLICE, to identify “hot spots” of increased interaction between strands. The model then looks at the frequency with which different genomic regions appear in the slice to infer information about the relative positions of genes and regions, called enhancers, that activate them.

"An analogy might be this—if you want to understand how school children interact you might take occasional photographs of where they sit in the canteen or appear together in the playground,” explained co-senior study investigator Ana Pombo, Ph.D., group head at the Max Delbrück Center and professor at Humboldt University of Berlin. "If you do that many times over a month, you will begin to see a pattern in those who often sit next to each other, or who run around together while playing. These random snapshots might tell you about their social interactions."

"This is made possible by filtering out random encounters from real interactions using mathematical methods," added co-senior study author Mario Nicodemi, Ph.D., professor of physics at the University of Napoli.

In the new study, the investigators applied the method to mouse embryonic stem cells, hoping it will help shed light on many genes whose activity is disturbed in some very serious diseases. For some disorders, the problem lies within the sequence of a gene, but defects in regulatory regions found elsewhere in the genome can be equally dangerous and much harder to understand. The new data provides a long list of new suspects that can now be scrutinized by researchers.

While previous studies have identified two-way contacts, this information does not reveal how often such contacts take place and by implication how important they might be. "They can spot that you and I are friends, but not how strong this friendship is, relative to everyone else," Dr. Pombo noted.

"People have measured two-way contacts for a long time," noted co-lead study author Robert Beagrie, Ph.D., who was a doctoral student in Dr. Pombo’s laboratory at the time and is now based at the University of Oxford. "Those studies have often shown that you can have a set of different DNA elements that interact with each other in pairs. With this new approach, we are able to generate a genome-wide catalog of all the regions that we are confident interact in groups."

Now, the researchers are able to reliably detect and quantify so-called "three-way contacts" in regions of the genome that are vigorously expressed. But perhaps the most notable advance through GAM is that experiments are based on single cells—whether common or scarce in a tissue—and can track their positions relative to each other within the tissue. Existing methods require lots of cells of the same type, which has made it difficult to study the biology and diseases of rare types.

"There is huge potential for applying this in human tissue samples to catalog contacts between regulatory regions and their target genes, and to use that to understand genetic variation and how it might alter aspects of nuclear biology," Dr. Pombo remarked.

Interestingly, some researchers are starting to show interest in using the technique to explore what happens when retroviruses insert their DNA into the genome of a host. Cancer scientists are also keen to create DNA maps of particular areas of a tumor.

"By exploiting the unique nature of GAM data, mathematical models can reliably derive such information, opening the way to identify multiple, group interactions that could play a key role in the regulation of genes," said Dr. Nicodemi.

"We can now ask whether a gene is contacted at the same time by all of its enhancers, or by each enhancer one at a time,” Dr. Beagrie concluded. "We know that many genes that are important for early development have multiple enhancers. But how and why they are acting to regulate genes remain unanswered questions."