Research expedition into the cell nucleus

What controls our genes? What mechanisms ensure that they are switched on or off at the right moment? Chromatin biologist Raffaella Santoro from the University of Zurich is seeking answers to these questions with her ERC project. Protocol of a meeting with a basic researcher.

Raffaella Santoro takes a piece of string and bundles it up. «You see, a chromosome in the nucleus of our cells looks something like this. Our genetic information, the DNA, is lined up on compactly twisted chromatin strings. In order to find space in the tiny cell nucleus, these strings fold again into complex bundles. This does not happen by chance. The structure that these bundles have and the place where they are located in the cell nucleus play an important role in the regulation of genes. But we don’t yet understand exactly what goes on there in detail, and that is what I’m trying to find out.»

We meet Raffaella Santoro in the office of her lab on the Irchel campus of the University of Zurich. The bright winter sun shines through the large window. We had asked the renowned chromatin researcher to explain to us her ERC research project, with which she wants to find out what controls the genes inside the cell nucleus and about the role the chromosome structure is playing in the process. With great patience and Italian charm, during the course of an afternoon, she opens a window into the fascinating world of her biological basic research to my photographer and myself.

The story behind wool threads in a plastic bowl

Raffaella Santoro puts the bundle of strings aside and places a plastic bowl on the table. Inside, colourful wool threads are grouped around a wobbly balloon filled with some water. «I made this simple model of a cell nucleus for you to explain my research,» she laughs and points to the rim of the bowl. «The plastic bowl represents the nuclear envelope. It is firm and has a membrane on each the inside and the outside separating the cell nucleus from the cytoplasm. The coloured balls of wool symbolise the different chromosomes that are placed at specific locations inside the nucleus. The flabby balloon between the wool balls stands for the small nuclear body, the nucleolus, which is found in every cell nucleus. Its form is flexible like a drop of oil in water. It also does not have a rigid wall and no membrane. But this unremarkable tiny thing plays a key role in the steering processes of life. Without the nucleolus we would probably not be here at all.» With the help of this colourful cell model, the top researcher then vividly explains to us what she is looking for and how she works.

As long as we are alive, the cells in our bodies are in continuous operation. They are constantly producing, rebuilding, dismantling and transporting proteins. The entire «blueprints» of these complex processes are recorded in the DNA, which is located on the chromosome strands. There, the required blueprints, the genes, are read as needed, copied as mRNA and transported into the cytoplasm of the cells, where they initiate the programmed processes. But how does the cell «know» when to switch which genes on and off and for how long? How does the steering mechanism work which ensures that the «right» sequences of the DNA are activated or deactivated at the «right» time? With her ERC research project, Raffaella Santoro has gained important new insights into this process.

«You see,» she says and points to one of the coloured wool threads of her cell nucleus model, «when the genes are activated, the section of the chromosome on which the switched-on genes are located is usually here, in the middle of the bundle. When the genes are inactive, we find the chromosomal section either near the nuclear envelope or directly at the nucleolus. We have now found that most DNA segments whose genes are switched off touch the nucleolus, while those genes that are active never actually touch it. This mechanism has the effect that the chromosome filament clusters change their structure again and again, depending on which genes are currently activated or deactivated. If we capture these constant structural changes of the chromosome bundles in snapshots, a dynamic three-dimensional map of the complex genome architecture in the cell nucleus emerges, which looks different depending on which genes are currently switched on or off. The current genome architecture reflects the current gene activities. And these differ from cell type to cell type. We have about 200 different types of cells in our body, all of them containing the same DNA. But depending on whether it is a brain, liver or blood cell, only those gene segments are activated that are important for the function of this cell type. The others are switched off.»

The enzyme trick

We have listened to Raffaella Santoro’s explanations with fascination and would now like to know, how she can determine which gene segments touch the nucleolus? To do this, the researcher first had to develop a method and test and validate it on stem cells from mice, whose epigenome and gene expression state is known. The crux of the matter was to find a way to mark the genes that touch the nucleolus. Raffaella Santoro and her technician Dominik Bär have succeeded in producing an enzyme that can be attached to the nucleolus. When a gene touches the nucleolus, the enzyme then puts a kind of stamp on it. A following DNA analysis shows which gene is involved. By comparing this with the known epigenome and gene expression status of the mice stem cells, it is possible to determine which functions the marked genes have and whether they are active or inactive. In this way, Raffaella Santoro’s research team has studied mice stem cells at different stages of their development and obtained a comprehensive picture of their dynamic genome structure.

But this is only the beginning. In the second part of her project, the bioscientist has now begun to apply this method to cancer cells. She wants to find out which genes of prostate cancer cells touch the nucleolus and are thus switched to inactive. And this is where Big Data comes into play. Her research team will match the empirical results with the large amount of data from prostate cancer research and clinical research to see if the identified genes play a role in prostate cancer.

Small and underrated

Raffaella Santoro has been researching the topic of prostate cancer for many years. Her method now opens up completely new possibilities for her. «We have found that the nucleolus of prostate cancer cells is much larger than that of normal prostate cells. When the nucleolus enlarges, the structure in the cell nucleus also changes. With our new method, we can now find out which genes are affected by these structural changes.» The ambitious scientist is thus laying another stepping stone on the long road to understanding the mechanisms that lead to prostate cancer. At the end of this road, it may one day be possible to develop novel therapies or even prevent the cancer.

But back to the nucleolus. The small nuclear body has occupied the creative biochemist again and again throughout her career and triggered the initial spark for her ERC project. «I have been fascinated by the nucleolus since my time as a postdoctoral researcher at the German Cancer Research Center in Heidelberg twenty years ago. We know that the nucleolus plays a key role in regulating life processes. But we still know little about its many functions. What is more, the study of its contents is highly complex.» For more than three years, Raffaella Santoro had been wondering how she could prove the interaction between genes and nucleolus. Finally, she had an idea. «I have this wonderful technician in my lab. So, I went to Dominik Bär and described to him that we needed a way to tag the genes that touch the nucleolus and that I had an idea how this could work. We did some experiments, created this enzyme and it worked!» Immediately, she wrote an application for an ERC Grant and received it.

Thanks to her ERC project, Raffaella Santoro can now focus intensely on the function of the nucleolus. In doing so, she and her team are also breaking new ground. One of her postdocs has specialised in cutting open the nucleolus of a single cell with a laser. The contents are sequenced and reveal new insights.

«So, is it possible to say that the nucleolus decides which genes are deactivated?», I try to summarise what we have learned. «No, this would be way too easy after all!», Raffaella Santoro states with feigned indignation and laughs. «We know that most of the genes that touch the nucleolus are inactive. But we do not know whether they are switched off because they touch the nucleolus or whether they touch the nucleolus because they are switched off. All we have at the moment is the correlation: genes that touch the nucleolus are inactive. To understand the reasons why, we need to know the mechanism behind it and in order to understand, we need to identify what causes a gene to touch the nucleolus and find out what happens to an inactive gene when it is no longer in contact with the nucleolus. But we are not that far yet.»
“And what happens next?”, I ask the passionate basic researcher at the end of this remarkable afternoon. “We will look at all aspects of the nucleolus in healthy and diseased cells and compare them until we understand the mechanisms,” she answers cheerfully.

Interview with Raffaella Santoro
Raffaella Santoro

Raffaella Santoro grew up in Rome. She studied Chemistry at the University of Rome La Sapienza und obtained her PhD there in Biochemistry. After her doctorate she went on to the Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute in Jena, Germany, in 1994, where she worked for three years as a postdoc. She then accepted a second postdoctoral position at the German Cancer Research Center in Heidelberg. In 2007, Raffaella Santoro moved to Zurich with her family and became Research Group Leader at the Department of Biosystems Science and Engineering (D-BSSE) of ETH Zurich. In 2009, she accepted an offer by the University of Zurich as Research Group Leader at today's Department of Molecular Mechanisms of Disease (DMMD), where she was appointed Professor of Epigenetics and Chromatin Dynamics in 2019. In her group «Santoro Lab», 15 researchers are currently working on understanding the basic principles of gene regulation.
In addition to her scientific work, Raffaella Santoro has been a passionate cook for some time. She loves to cook dishes from Rome and Central Italy, following recipes handed down from her mother and grandmother.

Horizon 2020 Project

NucleolusChromatin:  Analysis of the nucleolus in genome organization and function

  • Programme: ERC Advanced Grant
  • Duration: 1. September 2018 – 31. August 2023
    (60 months)
  • Contribution for University of Zurich: 2’500’000 €