<p>If not efficiently repaired, DNA double-stranded breaks can result in cell death. A major contributor to the repair of this DNA damage is the non-homologous end joining pathway (NHEJ) which depends on the proteins: X-ray cross complementing protein 4 (XRCC4) and XLF. These proteins form a complex that can bridge DNA substrates <em>in vitro. </em>Analysis of these proteins has demonstrated that the C-terminal region of XRCC4 is necessary for this bridging function. However, this region is also critical for both tetramerization and DNA binding abilities of XRCC4, making the interpretation of XRCC4's role in the DNA-bridging unclear. Here, we intend to further characterize the tetramerization of XRCC4 and find a functionally independent mutant. Our studies suggest that regions in the N-terminus of XRCC4 may be important for the tetramerization of the protein but not for its DNA binding ability. These mutants were also analyzed by circular dichroism and mobility shift assays to verify for the integrity of their secondary structure composition and show that they are able to interact with its known binding partner, DNA Ligase IV. Additionally, we have shown that the XRCC4:XLF complex as well as XLF alone are able to interact with DNA substrates as short as 36 base pairs. Taking the data together, we expect to be able to construct a structural model for the XRCC4:XLF complex with DNA and obtain a better understanding on the role of XRCC4’s tetramerization in the NHEJ pathway. As deficiency of XRCC4 has been implicated with tumourigenesis and immunodeficiency, understanding its role will be helpful for the development of treatments for such complications.</p> / Master of Science (MSc)

Clustered damage to DNA is a signature mark of radiation-induced damage, which involves damage to the nucleobases and/or DNA backbone. Double-strand breaks created by damaging agents are detrimental to cell survival leading to chromosomal translocations. Normal cells employ Non-homologous end-joining because of its faster kinetics, to suppress chromosomal translocations. However, the presence of complex DNA ends constitutes a significant challenge to NHEJ. Location of Thymine glycol (Tg) at DSB ends was a potential hindrance to end joining. The substrate with Tg at the third position (Tg3) from the DSB joined better than when present at the fifth position (Tg5). However, hNTH1 assay showed Tg5 to be a better substrate than Tg3 for BER, potentially explaining the increased Tg removal and decreased end joining of Tg5 in extracts. Nonetheless, there appeared to be no preference in the susceptibility of 5’-Tg substrates with Tg at the second and third positions from DSB ends. Polynucleotide kinase phosphatase is crucial in restoring the 3′ hydroxyl, and 5′ phosphate ends at strand breaks. No other enzyme is known to possess PNKP’s activity in mammalian cells at DSBs. Experiments done with PNKP knockout cells have shown some activity similar to PNKP, which appeared to be a part of NHEJ and was not pharmacologically inhibited by PNKP inhibitor. Additionally, core NHEJ factors XRCC4 and XLF influenced the activities of PNKP. Overall, these experiments suggest that Tg repair is dependent on the position from DSB and an alternative enzyme processes 3′- PO, and 5′-OH ends.

Au cours de leur développement, les cellules du système hématopoïétique sont très exposées aux dommages à l’ADN qui peuvent avoir une origine exogène ou endogène. Les organismes vivants ont développé de nombreux mécanismes de réparation pour y faire face, et leur dysfonctionnement est responsable de maladies rares mais sévères chez l’Homme. Un des deux mécanismes de réparation des cassures double-brin (CDB) de l’ADN joue un rôle prépondérant dans le développement du système immunitaire (SI) des mammifères. Il s’agit de la voie de réparation des extrémités non-homologues (NHEJ) qui est absolument essentiel au bon déroulement de la recombinaison V(D)J dans les progéniteurs lymphocytaires de la moelle osseuse et du thymus. En effet, la formation de CDB de l’ADN est une étape clé de ce remaniement. De même, bien que dans une moindre mesure, le NHEJ intervient pour réparer les cassures induites par AID lors de la commutation de classe des immunoglobulines (Ig- CSR). Notre équipe a précédemment identifié un nouveau facteur du NHEJ, Cernunnos (ou XLF), responsable chez l’Homme de déficit immunitaire combiné sévère (DCIS) associé à une sensibilité aux rayonnements ionisants (RI) et à une microcéphalie. Afin de mieux comprendre le rôle de Cernunnos dans le système hématopoïétique et dans le développement des lymphocytes en particulier, nous avons créé un modèle murin invalidé pour ce gène. De façon surprenante, le développement lymphocytaire se fait quasi normalement dans ces souris, le seul défaut observé est une diminution du nombre de lymphocytes. Cependant, l’analyse fine du répertoire des cellules T a permis de mettre en évidence un biais dans l’utilisation des segments variables V et J de la chaîne α du récepteur (TCRα). Ce serait là la signature d’un défaut de survie des thymocytes, passant par une activation chronique de la voie de l’apoptose dépendante de p53 en réponse à l’accumulation de dommages de l’ADN. Certaines sous- populations de lymphocytes T, comme les iNKTs et les MAITs, seraient ainsi affectées. Par ailleurs, notre équipe poursuit la caractérisation génétique et fonctionnelle de pathologies chez des patients dont le tableau clinique laisse penser qu’il existe un déficit immunitaire ou hématologique primaire associé à un défaut de réparation de l’ADN. Nous nous sommes intéressés à un patient dont le tableau clinique combinant déficit hématopoïétique et instabilité génomique suggère une origine génétique forte. Grâce aux techniques de séquençage haut- débit et à l’étude de ségrégation au sein de la famille nous avons pu isoler plusieurs mutations dont une nous a interpellé plus particulièrement / Throughout their development, hematopoietic cells are exposed to many DNA damages of either exogenous or endogenous origin. Living organisms evolved a variety of DNA repair mechanisms in order to face those threats, and their impairment leads to rare but severe diseases in human. Of the two mechanisms involved in the repair of DNA double-strand break (DSB) repair, one plays a major role in mammal’s Immune System (IS). The non-homologous end joining (NHEJ) pathway is essential for the correct proceeding of V(D)J recombination in lymphocyte progenitors from bone marrow and thymus. Indeed, the formation of DNA DSB is a key step of the rearrangement. In similar fashion, though to a lesser degree, NHEJ is involved in repair of AID induced breaks during immunoglobulin class switch recombination (Ig-CSR). Our team previously identified a new NHEJ factor, Cernunnos (or XLF), as being responsible for a human syndrome of severe combined immunodeficiency (SCID) associated with ionizing radiation (IR) sensitivity (RS-SCID) and microcephaly. To better understand Cernunnos role in the hematopoietic system and particularly in lymphocyte development, we engineered a knock-out (KO) mouse model for this gene. Surprisingly, lymphocyte development is almost normal in these mice, the only defect observed being a decrease of lymphocyte number. However, a refined analysis of T cell repertoire allowed us to uncover a bias in the use of V and J segments from the receptor’s α chain (TCRα). This is the signature of a survival defect in thymocytes, caused by chronic activation of the p53 dependent apoptosis pathway in response to DNA damage. Some discrete T cell populations, such as iNKTs and MAITS, would be affected. In the meantime, our team pursues the uncovering of genetic diseases and their functional description in patients showing signs of immune or hematopoietic deficiency combined to impaired DNA repair. We focused on a patient harboring clinical signs of genomic instability and hematopoietic defects with strong evidence for genetic cause. Thanks to high-throughput DNA sequencing technology and whole genome association study (WGAS), we identified several mutations, one of them striking us as pertinent

Les défauts dans la réparation des cassures double-brin de l'ADN (DSBs) peuvent avoir d'importantes conséquences pouvant entrainer une instabilité génomique et conduire à la mort cellulaire ou au développement de cancers. Dans la plupart des cellules mammifères, le mécanisme de Jonction des Extrémités Non Homologues (NHEJ) est le principal mécanisme de réparation des DSBs. L'ADN Ligase IV (LigIV) est une protéine unique dans sa capacité à promouvoir la NHEJ classique. Elle s'associe avec deux autres protéines structuralement similaires, XRCC4 et XLF (ou Cernunnos). LigIV interagit directement avec XRCC4 pour former un complexe stable, tandis que l'interaction entre XLF et ce complexe est médiée par XRCC4. XLF stimule fortement l'activité de ligation du complexe LigIV/XRCC4 par un mécanisme encore indéterminé. Récemment, un rôle structurel non catalytique a été attribué à LigIV (Cottarel et al., 2013). Dans le travail de thèse présenté ici, nous avons reconstitué l'étape de ligation de la NHEJ en utilisant des protéines recombinantes produites dans des bactéries afin d’une part, d'explorer les bases moléculaires du rôle structural de LigIV, d’autre part de comprendre le mécanisme par lequel XLF stimule le complexe de ligation, et enfin de mieux comprendre comment ces trois protéines coopèrent au cours de la NHEJ. Nos analyses biochimiques suggèrent que XLF via son interaction avec XRCC4 lié à LigIV, pourrait induire un changement conformationnel dans la LigIV. Ce réarrangement de la ligase exposerait son interface de liaison à l'ADN ce qui lui permettrait alors de ponter deux molécules indépendantes d'ADN, une capacité indépendante de l'activité catalytique de LigIV. / Failure to repair DNA double-strand breaks (DSBs) may have deleterious consequences inducing genomic instability and even cell death. In most mammalian cells, Non-Homologous End Joining (NHEJ) is a prominent DSB repair pathway. DNA ligase IV (LigIV) is unique in its ability to promote classical NHEJ. It associates with two structurally related proteins called XRCC4 and XLF (aka Cernunnos). LigIV directly interacts with XRCC4 forming a stable complex while the XLF interaction with this complex is mediated by XRCC4. XLF strongly stimulates the ligation activity of the LigIV/XRCC4 complex by an unknown mechanism. Recently, a structural noncatalytic role of LigIV has been uncovered (Cottarel et al., 2013). Here, we have reconstituted the end joining ligation step using recombinant proteins produced in bacteria to explore not only the molecular basis for the structural role of LigIV, but also to understand the mechanism by which XLF stimulates the ligation complex, and how these three proteins work together during NHEJ. Our biochemical analysis suggests that XLF, through interactions with LigIV/XRCC4 complex, could induce a conformational change in LigIV. Rearrangement of the LigIV would expose its DNA binding interface that is able to bridge two independent DNA molecules. This bridging ability is fully independent of LigIV’s catalytic activity. We have mutated this interface in order to attempt to disrupt the newly identified DNA bridging ability. In vitro analysis of this LigIV mutant will be presented as well as a preliminary in vivo analysis.

<p>DNA double-strand breaks pose a serious threat to genomic integrity. Double-strand breaks can cause chromosomal rearrangement, leading to uncontrolled cell proliferation, or even cell death. However, mammalian systems have in place the non-homologous end-joining pathway for repair of DNA double-strand breaks, which requires a core group of proteins to function: Ku70/80, DNA-PKcs, and Artemis for recognition, protection, and processing of the DNA ends, and XLF, XRCC4, and DNA LigaseIV for ligation of the DNA break. The work presented here focuses on the specific roles of XLF and XRCC4 within non-homologous end-joining. Initially, the structure of the N-terminal 224 residues of XLF was determined and found to consist of a head and tail domain, structurally homologous to XRCC4. Furthermore, L115 of XLF and K63, K65 and K99 of XRCC4 were identified as essential for an interaction between both proteins. This interaction was then shown to be required for stimulating ligation of mismatched DNA ends. To further understand how XRCC4 and XLF enhance LigaseIV activity, an XRCC4-XLF complex was crystallized. Truncated XRCC4 (1-157) was co-crystallized with truncated XLF (1-224), grown under conditions of decreasing temperature and increasing dehydration. The resulting structure at 3.94Å confirmed the necessity of L115 (XLF) and K63, K65 and K99 (XRCC4) to the XRCC4-XLF interaction, but also illustrated that XRCC4-XLF exists as an extended helical filament. DNA binding regions in both XRCC4 and XLF were also identified and used to construct a structural XRCC4-XLF-DNA binding model. Interestingly, XRCC4-DNA binding occurs in the same region of XRCC4 required for homo-tetramerization and binding to LigaseIV. These results culminate in a proposed model of non-homologous end-joining where XRCC4-XLF is involved not only in ligation of the double-strand break, but also in initial protection of the DNA ends.</p> / Doctor of Philosophy (PhD)