Protein posttranslational modifications by small ubiquitin-like modifiers (SUMOs) are critical for regulating a variety of cellular processes. Dysregulation of SUMOylation is increasingly... Show moreProtein posttranslational modifications by small ubiquitin-like modifiers (SUMOs) are critical for regulating a variety of cellular processes. Dysregulation of SUMOylation is increasingly associated with cancer and inhibitors that block SUMOylation are currently being explored as cancer treatment. We aimed to gain a better understanding of how the SUMO system governs the integrated network of nuclear signaling pathways, with a specific focus on genome maintenance. For this, we combined unbiased global mass spectrometry-based proteomics approaches with mechanistic follow-up studies. We found that the SUMO protease SENP6 maintains genome stability by ensuring the timely removal of SUMO chains on proteins involved in the response to DNA damage, affecting their localization, kinetics and nuclear condensation state. In addition, we found that noncovalent protein interactions with SUMOs mediated by SUMO-interaction motifs (SIMs) are also critical in maintaining genome stability, by facilitating the recruitment of DNA damage response proteins to the sites of damage. Lastly, we offer valuable new insights on noncovalent SUMO interactions by providing a comprehensive dataset of proteins that bind SUMO independently of the classical SUMO-SIM interaction. This suggests that the relevance of alternate modes of SUMO interactions is currently underestimated by the field and opens up new avenues for future research. Show less
This thesis addresses the repair of DNA double-strand breaks (DSBs) that arise in different contexts, both artificially inflicted DNA damage and spontaneously arising breaks. We have found that the... Show moreThis thesis addresses the repair of DNA double-strand breaks (DSBs) that arise in different contexts, both artificially inflicted DNA damage and spontaneously arising breaks. We have found that the (mutational) repair outcome of a DSB depends on the context in which it occurs. When cells are not replicating, DSBs are repaired via non-homologous end-joining (NHEJ). NHEJ efficiency can be affected by defective RNA processing. In replicating cells, the preferable mechanism for DSB repair is homologous recombination (HR). When canonical HR cannot be executed, because the repair template is not available (at G4-induced breaks, for example) or when not all HR factors are present (in BRCA1 deficient situations), alternative annealing is needed. This is carried out via polymerase theta-mediated end-joining (TMEJ), or when homologous nucleotides are available, via HELQ-1 mediated annealing of these homologous stretches. Finally, we have found that large tandem duplications can arise when break ends cannot anneal properly after the extension step in HR. Show less
Zinc-Finger (ZnF) proteins represent one of the most abundant group of proteins in the human genome. At first characterized as DNA binding proteins, it has become increasingly clear that ZnF... Show moreZinc-Finger (ZnF) proteins represent one of the most abundant group of proteins in the human genome. At first characterized as DNA binding proteins, it has become increasingly clear that ZnF-proteins have the ability to bind a large variety of substrates such as RNAs, proteins and post-translational modifications, suggesting potential roles in a variety of biological processes. Indeed, several studies have implicated ZnF-proteins for instance in transcription regulation, signal transduction and cell migration. Intriguingly, more recently these proteins have emerged as important protectors of the genome, particularly by orchestrating the repair of highly deleterious DNA double-strand breaks. Here we provide a comprehensive summary of the roles of ZnF domain-containing proteins in DNA double-strand break repair and discuss how their dysfunction impacts genome stability and human disease. Show less
DNA encodes the genetic instructions for living organisms. However, damage to the DNA is inevitable, because DNA itself is an unstable molecule and environmental factors such as UV-radiation or X... Show moreDNA encodes the genetic instructions for living organisms. However, damage to the DNA is inevitable, because DNA itself is an unstable molecule and environmental factors such as UV-radiation or X-rays cause damage to the DNA. A certain type of DNA damages can block DNA replication, an essential step before cell can divide. The polymerases that normally replicate DNA are incredibly efficient and virtually flawless on undamaged DNA, but they cannot replicate damaged DNA. In multi-celled organisms, the most important defense mechanism against this is Translesion DNA synthesis (TLS). TLS protects against various negative consequences of damage to the DNA. For this, TLS utilizes specialized TLS polymerases that can replicate damaged DNA.My experiments show that the strong evolutionary conservation of TLS is explained by the dual functions of TLS: guarding replication potential and genome stability. TLS suppresses genomic instability, by preventing conversion of replication blocks to double-stranded DNA breaks (DSBs). Without functional TLS, DSBs arise and result in larger and more harmful mutations. TLS is beneficial for organisms because it supports continuous reproduction and growth. Although DNA damage is always present and unavoidable, TLS guards against the formation of mutations that would otherwise lead to cancer, aging and congenital disease. Show less
