Thesis defense Erica Vos: Gene Control in 3D

Erica Vos from the De Laat group successfully defended her thesis “Gene control in 3D: The roles of CTCF and chromatin looping in organizing a functional genome” on the 31^st of October. During her PhD, Vos studied the role of 3D organization of DNA in controlling the activity of genes. In particular, she investigated the role of a specific protein, called CTCF.

Living things are made up of microscopic units called cells, which vary greatly in shape and behavior. Every cell within an organism contains the same genetic instructions, or DNA, packed in chromosomes. Only a tiny part of the amazingly long and complex set of human DNA molecules encodes genes, the instructions for making different types of cells (such as brain, heart, skin, etc.). Each cell type has a specific set of genes that are turned “on”. This set of genes that is turned “on”, or active, determines what kind of cell it is; a skin cell has a different set of active genes than a heart cell. Mistakes in the regulation of gene activity can lead to developmental disorders and disease, so studying the mechanisms that control gene activity will help us to better understand principles of life and disease and may guide future therapies.

Gene activity is partly controlled by how DNA is organized in the nucleus of each cell. For example, inactive genes are more tightly packed and less accessible, while active genes are more open. If a gene is physically close to a genetic switch called an enhancer, forming a DNA loop, this can boost a gene’s activity. Other DNA loops can prevent enhancers from turning on the wrong genes by making insulated structures called domains. Enhancers usually do not form loops with genes outside their domains, ensuring that the activity of genes is controlled only by specific enhancers.

CTCF proteins (green and red arrows) bound to the DNA (grey) enable the formation of domains, or large loops within which genes and enhancers can come together. The CTCF proteins need to be point towards each other for a loop to form. Copyright © Elsevier.

During her PhD, Vos aimed to better understand how DNA loops and domains form, and how these structures control gene activity. She investigated the role of the architectural protein CTCF in determining the direction in which loops form and experimentally confirmed the importance of CTCF binding orientation in this process. Disrupting CTCF binding or the orientation of binding can disrupt looping as well as the regulation of gene activity. Mutations in CTCF or its binding sites can lead to multiple diseases including cancer. A better understanding of the role of CTCF in the regulation of gene activity may therefore help to better understand what goes wrong in these diseases.

A single human cell in which a gene (green dot) and an enhancer (red dot) come together. Copyright © Hubrecht Institute, credit: Stijn Sonneveld and Erica Vos.

Together with researchers from the Tanenbaum group at the Hubrecht Institute, Vos also aimed to set up new microscopy tools. In the future, these tools may be used to determine the dynamics with which an enhancer and a gene come together and move apart, and at the same time study how gene activity is affected by this. “We’ve only started setting up the tools needed to microscopically quantify physical interactions between an enhancer and a gene,” says Vos, “but we are excited that the tools seem to be functional and we expect that these will enable us to closely examine the real-time relationship between enhancer-gene contacts and gene activity.”

Erica Vos has spent the past 6 years investigating gene regulation in 3D in the group of Wouter de Laat. After some well-deserved time off, she will start working at the ETH in Zürich, Switzerland. As a postdoc in the lab of Anton Wutz, she will study gene regulation in the context of the mammalian X chromosome.

Wouter de Laat is group leader at the Hubrecht Institute, professor of Biomedical Genomics at the UMC Utrecht and Oncode Investigator.