Developing new tools to study epigenetics in single cells and DNA molecules – PhD defense Joe Verity-Legg

Every person starts from a single cell, the fertilized egg. This cell divides many times and the new cells specialize to become tissues. The blueprints for making cells reside in our DNA. The first cell starts out with access to all the information to make a whole human, but the access to some of it is restricted as the cell divides. This is comparable to dropping courses in school: if you drop biology, you will likely not become a biologist. In the same way, a cell is less likely to become a muscle cell as it loses access to this information in the DNA.

The function of a cell is determined by which genesA small piece of DNA with a specific function. For example, genes determine which color our eyes have and whether we have curly or straight hair. In a human cell, the DNA contains about 30.000 genes, each having a specific function. Genes are hereditary and can therefore be passed on to offspring. are on and which are off. One way to control this is through epigenetics. Epigenetics consists of multiple layers, for example, chemical modification of the DNA or the proteins called ‘histones’ that DNA is wrapped around. These layers can interact with each other to form complex networks that control genes. Although it is known that these layers exist, it is not fully known how the individual layers function or how they interact with each other. This is partly because the technology required to research it was not invented yet.

Chiming in

“It’s a matter of building on those who have come before. You need to combine a lot of technologies and those technologies are still very young and new. Getting all of that information from one cell at a time means you have to have very sensitive technology,” Verity-Legg points out. With this in mind, he created a new tool during his PhD which he named ChIMe-seq. This tool can be used to measure three layers of epigenetic modification: DNA methylation, histone modification, and nucleosome positioning. With ChIMe-seq, researchers can measure these layers simultaneously in single cells or even single pieces of DNA. “By measuring all of these epigenetic layers at the same time, we can get a better idea of how they interact with each other,” Verity-Legg explains.

Bells and whistles?

But why is it so important to measure these layers at the same time in single cells or single pieces of DNA? Epigenetics is often studied in many cells at the same time because many technologies are not sensitive enough to measure single cells. However, this has some downsides. “Each cell is slightly different. If you study mixes of 1,000,000 cells you will just see an average,” Verity-Legg explains, “only the biggest differences between the groups are visible and lots of information is lost.”

In contrast, ChIMe-seq can show all the individual epigenetic modifications within one cell, or piece of DNA, and the interactions between epigenetic layers. “ChIMe-seq adds the value of being able to say that two states are definitely linked because it happens in a single cell or piece of DNA,” Verity-Legg says.

Development and disease

During his PhD, Verity-Legg used ChIMe-seq in gastruloids, a model for studying early human development. He discovered that two reciprocal systems for switching off genes help control early differentiation. “Embryonic cells start out covered by one epigenetic modification associated with genes being turned off, but poised, ready to be switched on. Soon after, as cells start specializing, another modification that is often associated with more permanently switching off genes is distributed which begins limiting access to certain parts of the DNA,” Verity-Legg explains.

In addition to this developmental research, ChIMe-seq has already helped study the disease mechanisms of cancer. Cancer is caused by genetic and epigenetic changes that cause uncontrolled growth of cells, which is a hallmark of the disease. By researching epigenetics, we may find a way to control this process and thus cancer. “I hope that such research can help produce meaningful progress in the understanding and treatment of cancer and other complex human diseases,” says Verity-Legg.

Freedom and failure

What Verity-Legg appreciated most about his PhD experience is the freedom he was given to explore ideas out of sheer curiosity. On the other hand, freedom can be tricky to deal with as shown by one of his biggest challenges: planning. “Sometimes experiments fail and it is not immediately clear why they fail, but when it finally does work, it is very rewarding,” Verity-Legg says. Which leads to his advice for aspiring and beginning PhD students: “Some things will fail. Fail quickly wherever possible.”

Something that inspired Verity-Legg is his collaborations. He was part of the Marie Curie network and visited many labs in different cities: Milan, Munich, Istanbul, Paris, and more. “I always enjoyed talking about research with other scientists. I started with 14 other PhD students and we all went to symposia and things together,” Verity-Legg reminisces.