Analysis of Complex Genome Interactions Using “GAM”

Before getting a color TV, people who had black-and-white televisions up to the 1980s had no idea what they were missing. A similar shift could happen in the field of genomics, where researchers at the Max Delbrück Center’s Berlin Institute of Medical Systems Biology (MDC-BIMSB) have created a method called Genome Architecture Mapping (“GAM”) to see within the genome and see it in dazzling technicolor.

According to a recent study by the Pombo team published in Nature Methods, GAM exposes details about the spatial architecture of the genome that are hidden to scientists who only use Hi-C, a workhorse tool created in 2009 to examine DNA interactions.

With a black-and-white TV, you can see the shapes but everything looks grey. But if you have a color TV and look at flowers, you realize that they are red, yellow, and white and we were unaware of it. Similarly, there is also information in the way the genome is folded in three-dimensions that we have not been aware of.”

Ana Pombo, Professor and Head, Epigenetic Regulation and Chromatin Architecture Lab, Max Delbrück Center

The structure of DNA can be used to understand the causes of both health and disease. The nucleus of the cells, which is about 10 mm in size, houses a genome that is 2 m long.

Exact packaging is used to ensure that regulatory DNA activates and deactivates the appropriate genes at the appropriate moments. This process can be hampered and disease can result from modifications to the three-dimensional arrangement.

We have known for a long time that diseases run in families. More recently, we have come to understand that a great deal of this predisposition is because we inherit DNA sequence variants from our parents that affect how our genes are switched on and off.”

Dr Robert Beagrie, Study Co-First Author and Molecular Biologist, University of Oxford

GAM Provides More Complex Information

Scientists can freeze and examine the connections between regulatory regions and genes using methods like Hi-C and GAM. In Hi-C, chromatin is split up into bits by enzymes and then reassembled so that, upon sequencing, two-way DNA connections can be seen.

In GAM, which the Pombo team initially described in “Nature” in 2017, researchers extract DNA from hundreds of individual cell nuclei using incredibly thin slices. To discover which of the regions interact, they sequence the DNA and statistically analyze the data.

The group developed a map of the three-dimensional interactions using this method. They discovered several new relationships when they compared this to earlier 3D maps of the genome made with Hi-C.

They could not figure out why until they noticed they were utilizing GAM to observe more complicated interactions and several DNA regions coming together at the same time.

These more complex contacts contain active genes, regulatory regions, and super enhancers, which regulate important genes that determine cell identity.”

Dr Christoph Thieme, Study Co-First Author and Senior Postdoctoral Fellow, Max Delbrück Center

Hi-C, in contrast, mostly recorded two-way interactions. As two out of every three contacts discovered by GAM were not visible using Hi-C, and vice versa, both approaches work well together.

Beagrie added, “I was super excited to see that we had uncovered a really strong effect. It is clear that these complex interactions were much more common than we had previously appreciated.”