Washington [US], June 20 : Researchers uncovered previously unknown information about the genome's spatial architecture by relying solely on Hi-C, a workhorse tool developed in 2009 to study DNA interactions.
The study was published in the journal, 'Nature Methods.'
"With a black-and-white TV, you can see the shapes but everything looks grey," says Professor Ana Pombo, a molecular biologist and head of the Epigenetic Regulation and Chromatin Architecture lab. "But if you have a colour TV and look at flowers, you realize that they are red, yellow and white and we were unaware of it. Similarly, there's also information in the way the genome is folded in three dimensions that we have not been aware of."
Understanding the structure of DNA can reveal the origins of health and disease. Our cells fit a 2-meter-long genome into a nucleus with a diameter of about 10 micrometres. The packaging is done precisely so that regulatory DNA interacts with the correct genes at the correct times, turning them on and off. Changes in three-dimensional configuration can disrupt this process and result in disease.
"We've known for a long time that diseases run in families," says Dr Robert Beagrie, co-first author of the study and a molecular biologist at the University of Oxford, formerly at the Pombo lab. "More recently, we've 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."
GAM provides more complex information
Techniques such as Hi-C and GAM allow scientists to freeze and study the interactions between regulatory sequences and genes. In Hi-C, chromatin is cut into pieces using enzymes and then glued together again in such a way that two-way DNA interactions are revealed upon sequencing. In GAM, first described by the Pombo team in "Nature" in 2017, scientists take hundreds of thin slices of nuclei, each from individual cells, and extract DNA from them. They sequence the DNA and statistically analyze the data to learn which regions interact.
Using this technique, the team created a map of the three-dimensional interactions. When they compared this with existing 3D maps of the genome created using Hi-C, they found many novel interactions. This puzzled them until they realized they were seeing more complex interactions using GAM, with multiple regions of DNA 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," says Dr Christoph Thieme, co-first author of the study and a senior postdoctoral fellow in the Pombo lab.
In comparison, Hi-C captured mostly two-way interactions. Both techniques are complementary as two in three contacts detected by GAM were not visible using Hi-C and vice-versa.
"I was super excited to see that we had uncovered a really strong effect," Beagrie says. "It is clear that these complex interactions were much more common than we had previously appreciated."
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