Periodic Reporting for period 4 - CHROMREP (Dissecting the chromatin response to DNA damage in silenced heterochromatin regions)
Reporting period: 2024-06-01 to 2025-05-31
Every cell in our body constantly faces threats that can damage its DNA—this might be caused by environmental stress, chemical exposure, or even normal cellular processes. To keep their DNA intact, cells have evolved a wide range of repair systems. Fixing DNA damage properly is essential—not only for the survival of individual cells, but also for preventing diseases like cancer. What is often overlooked is that our DNA isn’t stored in one uniform environment. Inside the cell’s nucleus, DNA is packaged into different “neighborhoods,” known as chromatin domains. Some areas are loosely packed and easy to access (called euchromatin), while others are tightly condensed and more difficult to reach (called heterochromatin). These differences in DNA packaging can influence how easily the repair systems find and fix DNA damage. In this project, we wanted to understand how these different DNA neighborhoods—especially the densely packed heterochromatin—affect the way cells detect and repair broken DNA. We focused on two types of heterochromatin: one that is always tightly packed (called constitutive heterochromatin), and one that can change its structure depending on the cell's needs (called facultative heterochromatin). To study this, we used fruit flies, a powerful model system for genetic research. We developed precise tools that allow us to create controlled DNA damage in specific regions of the fly’s genome, and then watch in real time how the cell responds. By combining these tools with advanced imaging and molecular analysis, we discovered new ways in which cells change the structure of heterochromatin to help repair DNA damage more efficiently. Understanding how cells repair DNA in these tightly packed regions is not just important for basic science—it also has implications for human health. Similar processes are at work in human cells, and problems with DNA repair in heterochromatin may contribute to cancer development. Our findings could eventually help us understand how tumors resist treatment and how we might design better therapies in the future by targeting these repair mechanisms.
We developed a variety of DNA damage systems in fruit fly tissue that allow for in-depth analysis of heterochromatin domain-specific repair responses. We have combined these systems with chromatin analyses and high-resolution live imaging to dissect the DNA damage-associated heterochromatin changes and determine their function in DNA damage repair. In addition to the systems in fruit flies, we have also developed a new, in vitro (test-tube) approach to be able to identify new proteins involved in repair of DNA damage in heterochromatin. Using these systems, we have identified a number of DNA damage responses specific to heterochromatin regions and have analysed these processes in more detail.
By developing several new DNA damage systems, we are in the unique position to determine how heterochromatin is responding to DNA damage using both high resolution live imaging of larval tissues as well as chromatin analyses at the site of DNA damage. We have identified a variety of DNA damage responses specific to densely packaged heterochromatin regions. More specifically, we find the processes involved in the repair of facultative heterochromatin genes (genes important for organismal development), as well as the repair of repetitive sequences within constitutive heterochromatin. Finally, we have assessed the role of these processes in the maintenance of genome stability in the eukaryotic nucleus by analysing chromosome structure and the accumulation of DNA mutations in the absence of these processes.